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Lorah MM, He K, Blaney L, Akob DM, Harris C, Tokranov A, Hopkins Z, Shedd BP. Anaerobic biodegradation of perfluorooctane sulfonate (PFOS) and microbial community composition in soil amended with a dechlorinating culture and chlorinated solvents. Sci Total Environ 2024; 932:172996. [PMID: 38719042 DOI: 10.1016/j.scitotenv.2024.172996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
Perfluorooctane sulfonate (PFOS), one of the most frequently detected per- and polyfluoroalkyl substances (PFAS) occurring in soil, surface water, and groundwater near sites contaminated with aqueous film-forming foam (AFFF), has proven to be recalcitrant to many destructive remedies, including chemical oxidation. We investigated the potential to utilize microbially mediated reduction (bioreduction) to degrade PFOS and other PFAS through addition of a known dehalogenating culture, WBC-2, to soil obtained from an AFFF-contaminated site. A substantial decrease in total mass of PFOS (soil and water) was observed in microcosms amended with WBC-2 and chlorinated volatile organic compound (cVOC) co-contaminants - 46.4 ± 11.0 % removal of PFOS over the 45-day experiment. In contrast, perfluorooctanoate (PFOA) and 6:2 fluorotelomer sulfonate (6:2 FTS) concentrations did not decrease in the same microcosms. The low or non-detectable concentrations of potential metabolites in full PFAS analyses, including after application of the total oxidizable precursor assay, indicated that defluorination occurred to non-fluorinated compounds or ultrashort-chain PFAS. Nevertheless, additional research on the metabolites and degradation pathways is needed. Population abundances of known dehalorespirers did not change with PFOS removal during the experiment, making their association with PFOS removal unclear. An increased abundance of sulfate reducers in the genus Desulfosporosinus (Firmicutes) and Sulfurospirillum (Campilobacterota) was observed with PFOS removal, most likely linked to initiation of biodegradation by desulfonation. These results have important implications for development of in situ bioremediation methods for PFAS and advancing knowledge of natural attenuation processes.
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Affiliation(s)
- Michelle M Lorah
- U.S. Geological Survey, Maryland-Delaware-D.C. Water Science Center, Baltimore, MD 21228, USA.
| | - Ke He
- University of Maryland Baltimore County, Department of Chemical, Biochemical, and Environmental Engineering, Baltimore, MD 21250, USA
| | - Lee Blaney
- University of Maryland Baltimore County, Department of Chemical, Biochemical, and Environmental Engineering, Baltimore, MD 21250, USA
| | - Denise M Akob
- U.S. Geological Survey, Geology, Energy, & Minerals Science Center, Reston, VA 20192, USA
| | - Cassandra Harris
- U.S. Geological Survey, Geology, Energy, & Minerals Science Center, Reston, VA 20192, USA
| | - Andrea Tokranov
- U.S. Geological Survey, New England Water Science Center, Pembroke, NH 03275, USA
| | - Zachary Hopkins
- U.S. Geological Survey, Eastern Ecological Science Center, Kearneysville, WV 25430, USA
| | - Brian P Shedd
- U.S. Army Corps of Engineers, U.S. DOD Environmental Programs Branch, Environmental Division, Headquarters, Washington, D.C. 20314, USA
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2
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Branco RHR, Meulepas RJW, Sekar P, van Veelen HPJ, Rijnaarts HHM, Sutton NB. Biostimulation with oxygen and electron donors supports micropollutant biodegradation in an experimentally simulated nitrate-reducing aquifer. Sci Total Environ 2024; 928:172339. [PMID: 38608893 DOI: 10.1016/j.scitotenv.2024.172339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/16/2024] [Accepted: 04/07/2024] [Indexed: 04/14/2024]
Abstract
The availability of suitable electron donors and acceptors limits micropollutant natural attenuation in oligotrophic groundwater. This study investigated how electron donors with different biodegradability (humics, dextran, acetate, and ammonium), and different oxygen concentrations affect the biodegradation of 15 micropollutants (initial concentration of each micropollutant = 50 μg/L) in simulated nitrate reducing aquifers. Tests mimicking nitrate reducing field conditions showed no micropollutant biodegradation, even with electron donor amendment. However, 2,4-dichlorophenoxyacetic acid and mecoprop were biodegraded under (micro)aerobic conditions with and without electron donor addition. The highest 2,4-dichlorophenoxyacetic acid and mecoprop biodegradation rates and removal efficiencies were obtained under fully aerobic conditions with amendment of an easily biodegradable electron donor. Under microaerobic conditions, however, amendment with easily biodegradable dissolved organic carbon (DOC) inhibited micropollutant biodegradation due to competition between micropollutants and DOC for the limited oxygen available. Microbial community composition was dictated by electron acceptor availability and electron donor amendment, not by micropollutant biodegradation. Low microbial community richness and diversity led to the absence of biodegradation of the other 13 micropollutants (such as bentazon, chloridazon, and carbamazepine). Finally, adaptation and potential growth of biofilms interactively determined the location of the micropollutant removal zone relative to the point of amendment. This study provides new insight on how to stimulate in situ micropollutant biodegradation to remediate oligotrophic groundwaters as well as possible limitations of this process.
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Affiliation(s)
- Rita H R Branco
- Environmental Technology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, P.O. Box 1113, 8900 CC Leeuwarden, the Netherlands
| | - Roel J W Meulepas
- Wetsus, European Centre of Excellence for Sustainable Water Technology, P.O. Box 1113, 8900 CC Leeuwarden, the Netherlands
| | - Priyadharshini Sekar
- Environmental Technology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands; Wetsus, European Centre of Excellence for Sustainable Water Technology, P.O. Box 1113, 8900 CC Leeuwarden, the Netherlands
| | - H Pieter J van Veelen
- Wetsus, European Centre of Excellence for Sustainable Water Technology, P.O. Box 1113, 8900 CC Leeuwarden, the Netherlands
| | - Huub H M Rijnaarts
- Environmental Technology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Nora B Sutton
- Environmental Technology, Wageningen University & Research, P.O. Box 47, 6700 AA Wageningen, the Netherlands.
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3
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de Vogel FA, Goudriaan M, Zettler ER, Niemann H, Eich A, Weber M, Lott C, Amaral-Zettler LA. Biodegradable plastics in Mediterranean coastal environments feature contrasting microbial succession. Sci Total Environ 2024; 928:172288. [PMID: 38599394 DOI: 10.1016/j.scitotenv.2024.172288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/09/2024] [Accepted: 04/05/2024] [Indexed: 04/12/2024]
Abstract
Plastic pollution of the ocean is a top environmental concern. Biodegradable plastics present a potential "solution" in combating the accumulation of plastic pollution, and their production is currently increasing. While these polymers will contribute to the future plastic marine debris budget, very little is known still about the behavior of biodegradable plastics in different natural environments. In this study, we molecularly profiled entire microbial communities on laboratory confirmed biodegradable polybutylene sebacate-co-terephthalate (PBSeT) and polyhydroxybutyrate (PHB) films, and non-biodegradable conventional low-density polyethylene (LDPE) films that were incubated in situ in three different coastal environments in the Mediterranean Sea. Samples from a pelagic, benthic, and eulittoral habitat were taken at five timepoints during an incubation period of 22 months. We assessed the presence of potential biodegrading bacterial and fungal taxa and contrasted them against previously published in situ disintegration data of these polymers. Scanning electron microscopy imaging complemented our molecular data. Putative plastic degraders occurred in all environments, but there was no obvious "core" of shared plastic-specific microbes. While communities varied between polymers, the habitat predominantly selected for the underlying communities. Observed disintegration patterns did not necessarily match community patterns of putative plastic degraders.
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Affiliation(s)
- Fons A de Vogel
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, the Netherlands
| | - Maaike Goudriaan
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, the Netherlands
| | - Erik R Zettler
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, the Netherlands
| | - Helge Niemann
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, the Netherlands; Faculty of Geosciences, Department of Earth Sciences, Utrecht University, P.O. Box 80.115, 3508 TC Utrecht, the Netherlands; CAGE-Centre for Arctic Gas Hydrate, Environment and Climate, Department of Geosciences, UiT the Arctic University of Norway, 9037 Tromsø, Norway
| | - Andreas Eich
- HYDRA Marine Sciences GmbH, D-77815 Bühl, Germany
| | - Miriam Weber
- HYDRA Marine Sciences GmbH, D-77815 Bühl, Germany
| | | | - Linda A Amaral-Zettler
- Department of Marine Microbiology and Biogeochemistry, NIOZ Royal Netherlands Institute for Sea Research, P.O. Box 59, 1790 AB Den Burg, the Netherlands; Department of Freshwater and Marine Ecology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94240, 1090 GE Amsterdam, the Netherlands.
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4
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Fiard M, Militon C, Sylvi L, Migeot J, Michaud E, Jézéquel R, Gilbert F, Bihannic I, Devesa J, Dirberg G, Cuny P. Uncovering potential mangrove microbial bioindicators to assess urban and agricultural pressures on Martinique island in the eastern Caribbean Sea. Sci Total Environ 2024; 928:172217. [PMID: 38583633 DOI: 10.1016/j.scitotenv.2024.172217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
Martinique's mangroves, which cover 1.85 ha of the island (<0.1 % of the total area), are considerably vulnerable to local urban, agricultural, and industrial pollutants. Unlike for temperate ecosystems, there are limited indicators that can be used to assess the anthropogenic pressures on mangroves. This study investigated four stations on Martinique Island, with each being subject to varying anthropogenic pressures. An analysis of mangrove sediment cores approximately 18 cm in depth revealed two primary types of pressures on Martinique mangroves: (i) an enrichment in organic matter in the two stations within the highly urbanized bay of Fort-de-France and (ii) agricultural pressure observed in the four studied mangrove stations. This pressure was characterized by contamination, exceeding the regulatory thresholds, with dieldrin, total DDT, and metals (As, Cu and Ni) found in phytosanitary products. The mangroves of Martinique are subjected to varying degrees of anthropogenic pressure, but all are subjected to contamination by organochlorine pesticides. Mangroves within the bay of Fort-de-France experience notably higher pressures compared to those in the island's northern and southern regions. In these contexts, the microbial communities exhibited distinct responses. The microbial biomass and the abundance of bacteria and archaea were higher in the two less-impacted stations, while in the mangrove of Fort-de-France, various phyla typically associated with polluted environments were more prevalent. These differences in the microbiota composition led to the identification of 65 taxa, including Acanthopleuribacteraceae, Spirochaetaceae, and Pirellulaceae, that could potentially serve as indicators of an anthropogenic influence on the mangrove sediments of Martinique Island.
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Affiliation(s)
- Maud Fiard
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Cécile Militon
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Léa Sylvi
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
| | - Jonathan Migeot
- Impact Mer consulting, expertise, and R&D firm, 20 rue Karukéra, 97200 Fort de France, Martinique/FWI, France.
| | - Emma Michaud
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Ronan Jézéquel
- CEDRE, 715 rue Alain Colas, 29218 Brest CEDEX 2, France.
| | - Franck Gilbert
- Laboratoire Écologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, Toulouse INP, Université Toulouse 3 - Paul Sabatier, Toulouse, France.
| | | | - Jeremy Devesa
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, 29280 Plouzané, France.
| | - Guillaume Dirberg
- Biologie des Organismes et Ecosystèmes Aquatiques (UMR 8067 BOREA) Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, IRD, UCN, UA, Rue Buffon, 75005 Paris, France.
| | - Philippe Cuny
- Aix Marseille Univ., Université de Toulon, CNRS, IRD, MIO, 13288 Marseille, France.
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Visser AN, Martin JD, Osenbrück K, Rügner H, Grathwohl P, Kappler A. In situ incubation of iron(II)-bearing minerals and Fe(0) reveals insights into metabolic flexibility of chemolithotrophic bacteria in a nitrate polluted karst aquifer. Sci Total Environ 2024; 926:172062. [PMID: 38554974 DOI: 10.1016/j.scitotenv.2024.172062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Groundwater nitrate pollution is a major reason for deteriorating water quality and threatens human and animal health. Yet, mitigating groundwater contamination naturally is often complicated since most aquifers are limited in bioavailable carbon. Since metabolically flexible microbes might have advantages for survival, this study presents a detailed description and first results on our modification of the BacTrap© method, aiming to determine the prevailing microbial community's potential to utilize chemolithotrophic pathways. Our microbial trapping devices (MTDs) were amended with four different iron sources and incubated in seven groundwater monitoring wells for ∼3 months to promote growth of nitrate-reducing Fe(II)-oxidizing bacteria (NRFeOxB) in a nitrate-contaminated karst aquifer. Phylogenetic analysis based on 16S rRNA gene sequences implies that the identity of the iron source influenced the microbial community's composition. In addition, high throughput amplicon sequencing revealed increased relative 16S rRNA gene abundances of OTUs affiliated to genera such as Thiobacillus, Rhodobacter, Pseudomonas, Albidiferax, and Sideroxydans. MTD-derived enrichments set up with Fe(II)/nitrate/acetate to isolate potential NRFeOxB, were dominated by e.g., Acidovorax spp., Paracoccus spp. and Propionivibrio spp. MTDs are a cost-effective approach for investigating microorganisms in groundwater and our data not only solidifies the MTD's capacity to provide insights into the metabolic flexibility of the aquifer's microbial community, but also substantiates its metabolic potential for anaerobic Fe(II) oxidation.
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Affiliation(s)
- Anna-Neva Visser
- GeoZentrum Nordbayern, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Germany; Department of Geosciences, University of Tübingen, Germany.
| | - Joseph D Martin
- Department of Biology, Terrestrial Ecology, University of Copenhagen, Denmark
| | - Karsten Osenbrück
- Department of Geosciences, University of Tübingen, Germany; Federal Institute for Geosciences and Natural Resources (BGR), Hannover, Germany
| | - Hermann Rügner
- Department of Geosciences, University of Tübingen, Germany
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6
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Zhu QZ, Yin X, Taubner H, Wendt J, Friedrich MW, Elvert M, Hinrichs KU, Middelburg JJ. Secondary production and priming reshape the organic matter composition in marine sediments. Sci Adv 2024; 10:eadm8096. [PMID: 38758798 DOI: 10.1126/sciadv.adm8096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 04/11/2024] [Indexed: 05/19/2024]
Abstract
Organic matter (OM) transformations in marine sediments play a crucial role in the global carbon cycle. However, secondary production and priming have been ignored in marine biogeochemistry. By incubating shelf sediments with various 13C-labeled algal substrates for 400 days, we show that ~65% of the lipids and ~20% of the proteins were mineralized by numerically minor heterotrophic bacteria as revealed by RNA stable isotope probing. Up to 11% of carbon from the algal lipids was transformed into the biomass of secondary producers as indicated by 13C incorporation in amino acids. This biomass turned over throughout the experiment, corresponding to dynamic microbial shifts. Algal lipid addition accelerated indigenous OM degradation by 2.5 to 6 times. This priming was driven by diverse heterotrophic bacteria and sulfur- and iron-cycling bacteria and, in turn, resulted in extra secondary production, which exceeded that stimulated by added substrates. These interactions between degradation, secondary production, and priming govern the eventual fate of OM in marine sediments.
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Affiliation(s)
- Qing-Zeng Zhu
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
| | - Xiuran Yin
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Haikou, China
| | - Heidi Taubner
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Jenny Wendt
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, Bremen, Germany
| | - Marcus Elvert
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Kai-Uwe Hinrichs
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Jack J Middelburg
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
- Department of Earth Sciences, Utrecht University, Utrecht, Netherlands
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7
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MacVittie S, Doroodian S, Alberto A, Sogin M. Microbiome depletion and recovery in the sea anemone, Exaiptasia diaphana, following antibiotic exposure. mSystems 2024:e0134223. [PMID: 38757963 DOI: 10.1128/msystems.01342-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
Microbial species that comprise host-associated microbiomes play an essential role in maintaining and mediating the health of plants and animals. While defining the role of individual or even complex communities is important toward quantifying the effect of the microbiome on host health, it is often challenging to develop causal studies that link microbial populations to changes in host fitness. Here, we investigated the impacts of reduced microbial load following antibiotic exposure on the fitness of the anemone, Exaiptasia diaphana and subsequent recovery of the host's microbiome. Anemones were exposed to two different types of antibiotic solutions for 3 weeks and subsequently held in sterilized seawater for a 3-week recovery period. Our results revealed that both antibiotic treatments reduced the overall microbial load during and up to 1 week post-treatment. The observed reduction in microbial load was coupled with reduced anemone biomass, halted asexual reproduction rates, and for one of the antibiotic treatments, the partial removal of the anemone's algal symbiont. Finally, our amplicon sequencing results of the 16S rRNA gene revealed that anemone bacterial composition only shifted in treated individuals during the recovery phase of the experiment, where we also observed a significant reduction in the overall diversity of the microbial community. Our work implies that the E. diaphana's microbiome contributes to host fitness and that the recovery of the host's microbiome following disturbance with antibiotics leads to a reduced, but stable microbial state.IMPORTANCEExaiptasia diaphana is an emerging model used to define the cellular and molecular mechanisms of coral-algal symbioses. E. diaphana also houses a diverse microbiome, consisting of hundreds of microbial partners with undefined function. Here, we applied antibiotics to quantify the impact of microbiome removal on host fitness as well as define trajectories in microbiome recovery following disturbance. We showed that reduction of the microbiome leads to negative impacts on host fitness, and that the microbiome does not recover to its original composition while held under aseptic conditions. Rather the microbiome becomes less diverse, but more consistent across individuals. Our work is important because it suggests that anemone microbiomes play a role in maintaining host fitness, that they are susceptible to disturbance events, and that it is possible to generate gnotobiotic individuals that can be leveraged in microbiome manipulation studies to investigate the role of individual species on host health.
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Affiliation(s)
- Sophie MacVittie
- Department of Molecular Cell Biology, University of California, Merced, California, USA
| | - Saam Doroodian
- Department of Molecular Cell Biology, University of California, Merced, California, USA
| | - Aaron Alberto
- Department of Molecular Cell Biology, University of California, Merced, California, USA
| | - Maggie Sogin
- Department of Molecular Cell Biology, University of California, Merced, California, USA
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Miché L, Dries A, Ammar IB, Davidson S, Cagnacci L, Combet-Blanc Y, Abecassis V, Penton Fernandez G, Christen P. Changes in chemical properties and microbial communities' composition of a forest litter-based biofertilizer produced through aerated solid-state culture under different oxygen conditions. Environ Sci Pollut Res Int 2024:10.1007/s11356-024-33629-8. [PMID: 38755473 DOI: 10.1007/s11356-024-33629-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 05/06/2024] [Indexed: 05/18/2024]
Abstract
Fermented forest litter (FFL) is a bioproduct used as biofertilizer for several decades in Eastern Asia and Latin America. It is locally handcrafted by farmers in anaerobic conditions by fermenting forest litter added with agricultural by-products such as whey, cereal bran, and molasses. The aim of this study was to characterize the FFL process and product through gas and liquid chromatography analyses. It also provides some highlights on the influence of O2 on this solid-state culture. Under anoxic condition, a maximum CO2 production rate (CDPR) of 0.41 mL/h∙g dry matter (dm) was reached after 8 days. The main volatile organic compounds (VOCs) were ethanol and ethyl acetate, with a production rate profile similar to CDPR. After 21 days of culture, no residual sucrose nor lactose was detected. Lactic and acetic acids reached 58.8 mg/g dm and 10.2 mg/g dm, respectively, ensuring the acidification of the matrix to a final pH of 4.72. A metabarcoding analysis revealed that heterolactic acid bacteria (Lentilactobacillus, Leuconostoc), homolactic acid bacteria (Lactococcus), and yeasts (Saccharomyces, Clavispora) were predominant. Predicted genes in the microbiome confirmed the potential link between detected bacteria and acids and VOCs produced. When O2 was fed to the cultures, final pH reached values up to 8.5. No significant amounts of lactic nor acetic acid were found. In addition, a strong shift in microbial communities was observed, with a predominance of Proteobacteria and molds, among which are potential pathogens like Fusarium species. This suggests that particular care must be brought to maintain anoxic conditions throughout the process.
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Affiliation(s)
- Lucie Miché
- IMBE, Aix Marseille Univ, Avignon Univ, CNRS, Marseille, IRD, France
| | - Alizée Dries
- IMBE, Aix Marseille Univ, Avignon Univ, CNRS, Marseille, IRD, France
| | - Inès Ben Ammar
- IMBE, Aix Marseille Univ, Avignon Univ, CNRS, Marseille, IRD, France
| | - Sylvain Davidson
- MIO, Aix Marseille Univ, Univ Toulon, CNRS, Marseille, IRD, France
| | - Loris Cagnacci
- IMBE, Aix Marseille Univ, Avignon Univ, CNRS, Marseille, IRD, France
| | | | | | | | - Pierre Christen
- IMBE, Aix Marseille Univ, Avignon Univ, CNRS, Marseille, IRD, France.
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9
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Zhang L, Yuan Y, Li C, Zhang Y, Sun H, Xu R, Liu Y. Biomineralization of phosphorus during anaerobic treatment of distillery wastewaters. Sci Total Environ 2024; 925:171431. [PMID: 38442755 DOI: 10.1016/j.scitotenv.2024.171431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024]
Abstract
This study addresses the pressing environmental concerns associated with the rapidly growing distillery industry, which is a significant contributor to wastewater generation. By focusing on the treatment of distillery wastewater using anaerobic digestion, this research explores the potential to convert organic materials into biofuels (methane). Moreover, the study aims to recover both methane and phosphorus from distillery wastewater in a single anaerobic reactor, which represents a novel and unexplored approach. Laboratory-scale experiments were conducted using mesophilic and thermophilic upflow anaerobic sludge blanket reactors. A key aspect of the study involved the implementation of a unique strategy: the mixing of centrate and spent caustic wastewater streams. This approach was intended to enhance treatment performance, manipulate the microbial community structure, and thereby optimizing the overall treatment performance. The integration of the centrate and spent caustic streams yielded remarkable co-benefits, resulting in significant biomethane production and efficient phosphorus precipitation. The study demonstrated a phosphorus removal efficiency of ∼60 % throughout the 130-140 days operation period. The recovery of phosphorus via the reactor sludge offers exciting opportunities for its utilization as a fertilizer or as a raw material within the phosphorus refinery industry. The biomethane produced during the treatment exhibits significant energy potential, estimated at 0.5 GJ/(m3 distillery wastewater).
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Affiliation(s)
- Lei Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada; School of Civil & Environmental Engineering, Queensland University of Technology, Brisbane, QLD, Australia
| | - Yiyang Yuan
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Chengyuan Li
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Yingdi Zhang
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Huijuan Sun
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada
| | - Rui Xu
- School of Metallurgy and Environment, Central South University, Changsha, China
| | - Yang Liu
- Department of Civil and Environmental Engineering, University of Alberta, Edmonton, Canada; School of Civil & Environmental Engineering, Queensland University of Technology, Brisbane, QLD, Australia.
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10
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Nishisaka CS, Ventura JP, Bais HP, Mendes R. Role of Bacillus subtilis exopolymeric genes in modulating rhizosphere microbiome assembly. Environ Microbiome 2024; 19:33. [PMID: 38745256 DOI: 10.1186/s40793-024-00567-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/07/2024] [Indexed: 05/16/2024]
Abstract
BACKGROUND Bacillus subtilis is well known for promoting plant growth and reducing abiotic and biotic stresses. Mutant gene-defective models can be created to understand important traits associated with rhizosphere fitness. This study aimed to analyze the role of exopolymeric genes in modulating tomato rhizosphere microbiome assembly under a gradient of soil microbiome diversities using the B. subtilis wild-type strain UD1022 and its corresponding mutant strain UD1022eps-TasA, which is defective in exopolysaccharide (EPS) and TasA protein production. RESULTS qPCR revealed that the B. subtilis UD1022eps-TasA- strain has a diminished capacity to colonize tomato roots in soils with diluted microbial diversity. The analysis of bacterial β-diversity revealed significant differences in bacterial and fungal community structures following inoculation with either the wild-type or mutant B. subtilis strains. The Verrucomicrobiota, Patescibacteria, and Nitrospirota phyla were more enriched with the wild-type strain inoculation than with the mutant inoculation. Co-occurrence analysis revealed that when the mutant was inoculated in tomato, the rhizosphere microbial community exhibited a lower level of modularity, fewer nodes, and fewer communities compared to communities inoculated with wild-type B. subtilis. CONCLUSION This study advances our understanding of the EPS and TasA genes, which are not only important for root colonization but also play a significant role in shaping rhizosphere microbiome assembly. Future research should concentrate on specific microbiome genetic traits and their implications for rhizosphere colonization, coupled with rhizosphere microbiome modulation. These efforts will be crucial for optimizing PGPR-based approaches in agriculture.
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Affiliation(s)
- Caroline Sayuri Nishisaka
- Embrapa Environment, Jaguariúna, SP, Brazil
- Graduate Program in Agricultural Microbiology, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - João Paulo Ventura
- Embrapa Environment, Jaguariúna, SP, Brazil
- Graduate Program in Agricultural Microbiology, College of Agriculture "Luiz de Queiroz", University of São Paulo, Piracicaba, SP, Brazil
| | - Harsh P Bais
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, USA
- Ammon Pinizzotto Biopharmaceutical Innovation Center (BPI), Newark, DE, USA
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Pereira H, Chakarov N, Hoffman JI, Rinaud T, Ottensmann M, Gladow KP, Tobias B, Caspers BA, Maraci Ö, Krüger O. Early-life factors shaping the gut microbiota of Common buzzard nestlings. Anim Microbiome 2024; 6:27. [PMID: 38745254 DOI: 10.1186/s42523-024-00313-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/01/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Exploring the dynamics of gut microbiome colonisation during early-life stages is important for understanding the potential impact of microbes on host development and fitness. Evidence from model organisms suggests a crucial early-life phase when shifts in gut microbiota can lead to immune dysregulation and reduced host condition. However, our understanding of gut microbiota colonisation in long-lived vertebrates, especially during early development, remains limited. We therefore used a wild population of common buzzard nestlings (Buteo buteo) to investigate connections between the early-life gut microbiota colonisation, environmental and host factors. RESULTS We targeted both bacterial and eukaryotic microbiota using the 16S and 28S rRNA genes. We sampled the individuals during early developmental stages in a longitudinal design. Our data revealed that age significantly affected microbial diversity and composition. Nest environment was a notable predictor of microbiota composition, with particularly eukaryotic communities differing between habitats occupied by the hosts. Nestling condition and infection with the blood parasite Leucocytozoon predicted microbial community composition. CONCLUSION Our findings emphasise the importance of studying microbiome dynamics to capture changes occurring during ontogeny. They highlight the role of microbial communities in reflecting host health and the importance of the nest environment for the developing nestling microbiome. Overall, this study contributes to understanding the complex interplay between microbial communities, host factors, and environmental variables, and sheds light on the ecological processes governing gut microbial colonisation during early-life stages.
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Affiliation(s)
- Hugo Pereira
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany.
| | - Nayden Chakarov
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Joseph I Hoffman
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Department of Evolutionary Population Genetics, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- British Antarctic Survey, High Cross, Madingley Road, Cambridge, CB3 OET, UK
| | - Tony Rinaud
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Meinolf Ottensmann
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Kai-Philipp Gladow
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Busche Tobias
- Medical School East Westphalia-Lippe & Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, NRW, Germany
| | - Barbara A Caspers
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Öncü Maraci
- Department of Behavioural Ecology, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
| | - Oliver Krüger
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, 33615, Bielefeld, NRW, Germany
- Joint Institute for Individualisation in a Changing Environment (JICE), Bielefeld University and University of Münster, Konsequenz 45, 33615, Bielefeld, NRW, Germany
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12
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Benalcazar P, Seuradge B, Diochon AC, Kolka RK, Phillips LA. Conversion of boreal forests to agricultural systems: soil microbial responses along a land-conversion chronosequence. Environ Microbiome 2024; 19:32. [PMID: 38734653 PMCID: PMC11088160 DOI: 10.1186/s40793-024-00576-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND Boreal regions are warming at more than double the global average, creating opportunities for the northward expansion of agriculture. Expanding agricultural production in these regions will involve the conversion of boreal forests to agricultural fields, with cumulative impacts on soil microbial communities and associated biogeochemical cycling processes. Understanding the magnitude or rate of change that will occur with these biological processes will provide information that will enable these regions to be developed in a more sustainable manner, including managing carbon and nitrogen losses. This study, based in the southern boreal region of Canada where agricultural expansion has been occurring for decades, used a paired forest-adjacent agricultural field approach to quantify how soil microbial communities and functions were altered at three different stages post-conversion (< 10, > 10 and < 50, and > 50 years). Soil microbial functional capacity was assessed by quantitative PCR of genes associated with carbon (C), nitrogen, and phosphorous (P) cycling; microbial taxonomic diversity and community structure was assessed by amplicon sequencing. RESULTS Fungal alpha diversity did not change, but communities shifted from Basidiomycota to Ascomycota dominant within the first decade. Bacterial alpha diversity increased, with Gemmatimonadota groups generally increasing and Actinomycetota groups generally decreasing in agricultural soils. These altered communities led to altered functional capacity. Functional genes associated with nitrification and low molecular weight C cycling potential increased after conversion, while those associated with organic P mineralization potential decreased. Stable increases in most N cycling functions occurred within the first decade, but C cycling functions were still changing 50 years post conversion. CONCLUSIONS Microbial communities underwent a rapid shift in the first decade, followed by several decades of slower transition until stabilizing 50 years post conversion. Understanding how the microbial communities respond at different stages post-conversion improves our ability to predict C and N losses from emerging boreal agricultural systems, and provides insight into how best to manage these soils in a way that is sustainable at the local level and within a global context.
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Affiliation(s)
- Paul Benalcazar
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, ON, Canada
| | - Brent Seuradge
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, ON, Canada
| | - Amanda C Diochon
- Department of Geology, Lakehead University, Thunder Bay, ON, Canada
| | - Randall K Kolka
- USDA Forest Services Northern Research Station, Grand Rapid, MN, 55744, USA
| | - Lori A Phillips
- Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, ON, Canada.
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Mukherjee I, Grujčić V, Salcher MM, Znachor P, Seďa J, Devetter M, Rychtecký P, Šimek K, Shabarova T. Integrating depth-dependent protist dynamics and microbial interactions in spring succession of a freshwater reservoir. Environ Microbiome 2024; 19:31. [PMID: 38720385 PMCID: PMC11080224 DOI: 10.1186/s40793-024-00574-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Protists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes and energy transfer in freshwaters. Despite their significance, there is a notable gap in research on protistan dynamics, particularly in the deeper strata of temperate lakes. This study aimed to address this gap by integrating protists into the well-described spring dynamics of Římov reservoir, Czech Republic. Over a 2-month period covering transition from mixing to established stratification, we collected water samples from three reservoir depths (0.5, 10 and 30 m) with a frequency of up to three times per week. Microbial eukaryotic and prokaryotic communities were analysed using SSU rRNA gene amplicon sequencing and dominant protistan groups were enumerated by Catalysed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). Additionally, we collected samples for water chemistry, phyto- and zooplankton composition analyses. RESULTS Following the rapid changes in environmental and biotic parameters during spring, protistan and bacterial communities displayed swift transitions from a homogeneous community to distinct strata-specific communities. A prevalence of auto- and mixotrophic protists dominated by cryptophytes was associated with spring algal bloom-specialized bacteria in the epilimnion. In contrast, the meta- and hypolimnion showcased a development of a protist community dominated by putative parasitic Perkinsozoa, detritus or particle-associated ciliates, cercozoans, telonemids and excavate protists (Kinetoplastida), co-occurring with bacteria associated with lake snow. CONCLUSIONS Our high-resolution sampling matching the typical doubling time of microbes along with the combined microscopic and molecular approach and inclusion of all main components of the microbial food web allowed us to unveil depth-specific populations' successions and interactions in a deep lentic ecosystem.
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Affiliation(s)
- Indranil Mukherjee
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic.
| | - Vesna Grujčić
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Michaela M Salcher
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
| | - Petr Znachor
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005, Ceske Budejovice, Czech Republic
| | - Jaromír Seďa
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
| | - Miloslav Devetter
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology and Biogeochemistry, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
| | - Pavel Rychtecký
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
| | - Karel Šimek
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005, Ceske Budejovice, Czech Republic
| | - Tanja Shabarova
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic.
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Perdigão R, Tomasino MP, Magalhães C, Carvalho MF, Almeida CMR, Mucha AP. Microbial response to a port fuel spill: Community dynamics and potential for bioremediation. Mar Pollut Bull 2024; 203:116434. [PMID: 38713928 DOI: 10.1016/j.marpolbul.2024.116434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/09/2024]
Abstract
Following a fuel leakage inside a Portuguese maritime port, we conducted parallel 30-day experiments using contaminated seawater and fuel, sampled five days after the incident. This study aimed to (i)survey the native microbial community response to the spilled fuel and (ii)evaluate the efficacy of bioremediation, both biostimulation and bioaugmentation with a lyophilized bacterial consortium (Rhodococcus erythropolis, Pseudomonas sp.), in accelerating hydrocarbon degradation. Metabarcoding analysis revealed a shift in microbial communities, with increased abundance of hydrocarbon-degraders (e.g. Alcanivorax, Thalassospira). Ninety-five hydrocarbonoclastic bacteria were isolated, including key groups from the enriched communities. The lyophilized bacteria added in bioaugmentation, enhanced the abundance of hydrocarbon-degraders over time and were recovered throughout time. Bioremediation treatments favoured biodegradation, achieving over 60 % removal of total petroleum hydrocarbons after 15 days, contrasting with natural attenuation where almost no TPH was removed. This work highlights the potential of bioremediation technologies to accelerate hydrocarbon-degrading activity, for oil spills inside ports.
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Affiliation(s)
- Rafaela Perdigão
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal; School of Medicine and Biomedical Sciences, University of Porto, Rua de Jorge Viterbo Ferreira, 228, Porto 4050-313, Portugal.
| | - Maria Paola Tomasino
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal.
| | - Catarina Magalhães
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal; Faculty of Sciences, University of Porto, Rua do Campo Alegre 790, Porto 4150-171, Portugal.
| | - Maria F Carvalho
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal; School of Medicine and Biomedical Sciences, University of Porto, Rua de Jorge Viterbo Ferreira, 228, Porto 4050-313, Portugal.
| | - C Marisa R Almeida
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal; Faculty of Sciences, University of Porto, Rua do Campo Alegre 790, Porto 4150-171, Portugal.
| | - Ana P Mucha
- Interdisciplinary Centre of Marine and Environmental Research of the University of Porto, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos, S/N, Matosinhos 4450-208, Portugal; Faculty of Sciences, University of Porto, Rua do Campo Alegre 790, Porto 4150-171, Portugal.
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Blais MA, Vincent WF, Vigneron A, Labarre A, Matveev A, Coelho LF, Lovejoy C. Diverse winter communities and biogeochemical cycling potential in the under-ice microbial plankton of a subarctic river-to-sea continuum. Microbiol Spectr 2024; 12:e0416023. [PMID: 38511950 DOI: 10.1128/spectrum.04160-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Winter conditions greatly alter the limnological properties of lotic ecosystems and the availability of nutrients, carbon, and energy resources for microbial processes. However, the composition and metabolic capabilities of winter microbial communities are still largely uncharacterized. Here, we sampled the winter under-ice microbiome of the Great Whale River (Nunavik, Canada) and its discharge plume into Hudson Bay. We used a combination of 16S and 18S rRNA gene amplicon analysis and metagenomic sequencing to evaluate the size-fractionated composition and functional potential of the microbial plankton. These under-ice communities were diverse in taxonomic composition and metabolically versatile in terms of energy and carbon acquisition, including the capacity to carry out phototrophic processes and degrade aromatic organic matter. Limnological properties, community composition, and metabolic potential differed between shallow and deeper sites in the river, and between fresh and brackish water in the vertical profile of the plume. Community composition also varied by size fraction, with a greater richness of prokaryotes in the larger size fraction (>3 µm) and of microbial eukaryotes in the smaller size fraction (0.22-3 µm). The freshwater communities included cosmopolitan bacterial genera that were previously detected in the summer, indicating their persistence over time in a wide range of physico-chemical conditions. These observations imply that the microbial communities of subarctic rivers and their associated discharge plumes retain a broad taxonomic and functional diversity throughout the year and that microbial processing of complex terrestrial materials persists beneath the ice during the long winter season. IMPORTANCE Microbiomes vary over multiple timescales, with short- and long-term changes in the physico-chemical environment. However, there is a scarcity of data and understanding about the structure and functioning of aquatic ecosystems during winter relative to summer. This is especially the case for seasonally ice-covered rivers, limiting our understanding of these ecosystems that are common throughout the boreal, subpolar, and polar regions. Here, we examined the winter under-ice microbiome of a Canadian subarctic river and its entry to the sea to characterize the taxonomic and functional features of the microbial community. We found substantial diversity in both composition and functional capabilities, including the capacity to degrade complex terrestrial compounds, despite the constraints imposed by a prolonged seasonal ice-cover and near-freezing water temperatures. This study indicates the ecological complexity and importance of winter microbiomes in ice-covered rivers and the coastal marine environment that they discharge into.
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Affiliation(s)
- Marie-Amélie Blais
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Warwick F Vincent
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Adrien Vigneron
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Aurélie Labarre
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
- Québec-Océan, Université Laval, Quebec City, Quebec, Canada
| | - Alex Matveev
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Centre for Northern Studies (CEN), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
| | - Lígia Fonseca Coelho
- Centro de Química Estrutural, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
- Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Connie Lovejoy
- Département de Biologie, Université Laval, Quebec City, Quebec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Quebec, Canada
- Takuvik Joint International Laboratory, Université Laval, Quebec City, Quebec, Canada
- Québec-Océan, Université Laval, Quebec City, Quebec, Canada
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Vilardi KJ, Johnston J, Dai Z, Cotto I, Tuttle E, Patterson A, Stubbins A, Pieper KJ, Pinto AJ. Nitrogen source influences the interactions of comammox bacteria with aerobic nitrifiers. Microbiol Spectr 2024; 12:e0318123. [PMID: 38511951 PMCID: PMC11064514 DOI: 10.1128/spectrum.03181-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 02/29/2024] [Indexed: 03/22/2024] Open
Abstract
While the co-existence of comammox Nitrospira with canonical nitrifiers is well documented in diverse ecosystems, there is still a dearth of knowledge about the mechanisms underpinning their interactions. Understanding these interaction mechanisms is important as they may play a critical role in governing nitrogen biotransformation in natural and engineered ecosystems. In this study, we tested the ability of two environmentally relevant factors (nitrogen source and availability) to shape interactions between strict ammonia and nitrite-oxidizing bacteria and comammox Nitrospira in continuous flow column reactors. The composition of inorganic nitrogen species in reactors fed either ammonia or urea was similar during the lowest input nitrogen concentration (1 mg-N/L), but higher concentrations (2 and 4 mg-N/L) promoted significant differences in nitrogen species composition and nitrifier abundances. The abundance and diversity of comammox Nitrospira were dependent on both nitrogen source and input concentrations as multiple comammox Nitrospira populations were preferentially enriched in the urea-fed system. In contrast, their abundance was reduced in response to higher nitrogen concentrations in the ammonia-fed system. The preferential enrichment of comammox Nitrospira in the urea-fed system could be associated with their ureolytic activity calibrated to their ammonia oxidation rates, thus minimizing ammonia accumulation, which may be partially inhibitory. However, an increased abundance of comammox Nitrospira was not associated with a reduced abundance of nitrite oxidizers in the urea-fed system while a negative correlation was found between them in the ammonia-fed system, the latter dynamic likely emerging from reduced availability of nitrite to strict nitrite oxidizers at low ammonia concentrations. IMPORTANCE Nitrification is an essential biological process in drinking water and wastewater treatment systems for treating nitrogen pollution. The discovery of comammox Nitrospira and their detection alongside canonical nitrifiers in these engineered ecosystems have made it necessary to understand the environmental conditions that regulate their abundance and activity relative to other better-studied nitrifiers. This study aimed to evaluate two important factors that could potentially influence the behavior of nitrifying bacteria and, therefore, impact nitrification processes. Column reactors fed with either ammonia or urea were systematically monitored to capture changes in nitrogen biotransformation and the nitrifying community as a function of influent nitrogen concentration, nitrogen source, and reactor depth. Our findings show that with increased ammonia availability, comammox Nitrospira decreased in abundance while nitrite oxidizers abundance increased. Yet, in systems with increasing urea availability, comammox Nitrospira abundance and diversity increased without an associated reduction in the abundance of canonical nitrifiers.
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Affiliation(s)
- Katherine Jeanne Vilardi
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts, USA
| | - Juliet Johnston
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Zihan Dai
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Irmarie Cotto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Erin Tuttle
- Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts, USA
| | - Ariana Patterson
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts, USA
| | - Aron Stubbins
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts, USA
- Department of Marine and Environmental Sciences, Northeastern University, Boston, Massachusetts, USA
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Kelsey J. Pieper
- Department of Civil and Environmental Engineering, Northeastern University, Boston, Massachusetts, USA
| | - Ameet J. Pinto
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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Avendaño KA, Ponce-Jahen SJ, Valenzuela EI, Pajares S, Samperio-Ramos G, Camacho-Ibar VF, Cervantes FJ. Nitrogen loss in coastal sediments driven by anaerobic ammonium oxidation coupled to microbial reduction of Mn(IV)-oxide. Sci Total Environ 2024; 923:171368. [PMID: 38438040 DOI: 10.1016/j.scitotenv.2024.171368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/06/2024]
Abstract
Coastal sediments play a central role in regulating the amount of land-derived reactive nitrogen (Nr) entering the ocean, and their importance becomes crucial in vulnerable ecosystems threatened by anthropogenic activities. Sedimentary denitrification has been identified as the main sink of Nr in marine environments, while anaerobic ammonium oxidation with nitrite (anammox) has also been pointed out as a key player in controlling the nitrogen pool in these locations. Collected evidence in the present work indicates that the microbial biota in coastal sediments from Baja California (northwestern Mexico) has the potential to drive anaerobic ammonium oxidation linked to Mn(IV) reduction (manganammox). Unamended sediment showed ammonification, but addition of vernadite (δMnO2 with nano-crystal size ∼15 Å) as terminal electron acceptor fueled simultaneous ammonium oxidation (up to ∼400 μM of ammonium removed) and production of Mn(II) with a ratio ∆[Mn(II)]/∆[NH4+] of 1.8, which is very close to the stoichiometric value of manganammox (1.5). Additional incubations spiked with external ammonium also showed concomitant ammonium oxidation and Mn(II) production, accounting for ∼30 % of the oxidized ammonium. Tracer analysis revealed that the nitrogen loss associated with manganammox was 4.2 ± 0.4 μg 30N2/g-day, which is 17-fold higher than that related to the feammox process (anaerobic ammonium oxidation linked to Fe(III) reduction, 0.24 ± 0.02 μg 30N2/g-day). Taxonomic characterization based on 16S rRNA gene sequencing revealed the existence of several clades belonging to Desulfobacterota as potential microorganisms catalyzing the manganammox process. These findings suggest that manganammox has the potential to be an additional Nr sink in coastal environments, whose contribution to total Nr losses remains to be evaluated.
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Affiliation(s)
- Karen A Avendaño
- Laboratory for Research on Advanced Processes for Water Treatment, Engineering Institute, Campus Juriquilla, Universidad Nacional Autónoma de México, Blvd. Juriquilla 2001, 76230 Querétaro, Mexico
| | - Sergio J Ponce-Jahen
- Laboratory for Research on Advanced Processes for Water Treatment, Engineering Institute, Campus Juriquilla, Universidad Nacional Autónoma de México, Blvd. Juriquilla 2001, 76230 Querétaro, Mexico
| | - Edgardo I Valenzuela
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Campus Puebla, Atlixcáyotl 5718, Reserva Territorial Atlixcáyotl, Puebla 72453, Mexico
| | - Silvia Pajares
- Unidad Académica de Ecología y Biodiversidad Acuática, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Guillermo Samperio-Ramos
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Ensenada, Mexico
| | - Víctor F Camacho-Ibar
- Instituto de Investigaciones Oceanológicas, Universidad Autónoma de Baja California, Ensenada, Mexico
| | - Francisco J Cervantes
- Laboratory for Research on Advanced Processes for Water Treatment, Engineering Institute, Campus Juriquilla, Universidad Nacional Autónoma de México, Blvd. Juriquilla 2001, 76230 Querétaro, Mexico.
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Martinez Boggio G, Monteiro HF, Lima FS, Figueiredo CC, Bisinotto RS, Santos JEP, Mion B, Schenkel FS, Ribeiro ES, Weigel KA, Peñagaricano F. Host and rumen microbiome contributions to feed efficiency traits in Holstein cows. J Dairy Sci 2024; 107:3090-3103. [PMID: 38135048 DOI: 10.3168/jds.2023-23869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023]
Abstract
It is now widely accepted that dairy cow performance is influenced by both the host genome and rumen microbiome composition. The contributions of the genome and the microbiome to the phenotypes of interest are quantified by heritability (h2) and microbiability (m2), respectively. However, if the genome and microbiome are included in the model, then the h2 reflects only the contribution of the direct genetic effects quantified as direct heritability (hd2), and the holobiont effect reflects the joint action of the genome and the microbiome, quantified as the holobiability (ho2). The objectives of this study were to estimate h2, hd2,m2, and ho2 for dry matter intake, milk energy, and residual feed intake; and to evaluate the predictive ability of different models, including genome, microbiome, and their interaction. Data consisted of feed efficiency records, SNP genotype data, and 16S rRNA rumen microbial abundances from 448 mid-lactation Holstein cows from 2 research farms. Three kernel models were fit to each trait: one with only the genomic effect (model G), one with the genomic and microbiome effects (model GM), and one with the genomic, microbiome, and interaction effects (model GMO). The model GMO, or holobiont model, showed the best goodness-of-fit. The hd2 estimates were always 10% to 15% lower than h2 estimates for all traits, suggesting a mediated genetic effect through the rumen microbiome, and m2 estimates were moderate for all traits, and up to 26% for milk energy. The ho2 was greater than the sum of hd2 and m2, suggesting that the genome-by-microbiome interaction had a sizable effect on feed efficiency. Kernel models fitting the rumen microbiome (i.e., models GM and GMO) showed larger predictive correlations and smaller prediction bias than the model G. These findings reveal a moderate contribution of the rumen microbiome to feed efficiency traits in lactating Holstein cows and strongly suggest that the rumen microbiome mediates part of the host genetic effect.
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Affiliation(s)
| | - Hugo F Monteiro
- Department of Population Health and Reproduction, University of California, Davis, Davis, CA 95616
| | - Fabio S Lima
- Department of Population Health and Reproduction, University of California, Davis, Davis, CA 95616
| | - Caio C Figueiredo
- Department of Veterinary Clinical Sciences, Washington State University, Pullman, WA 99163
| | - Rafael S Bisinotto
- Department of Large Animal Clinical Sciences, University of Florida, Gainesville, FL 32610
| | - José E P Santos
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611
| | - Bruna Mion
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G-2W1
| | - Flavio S Schenkel
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G-2W1
| | - Eduardo S Ribeiro
- Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada N1G-2W1
| | - Kent A Weigel
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706
| | - Francisco Peñagaricano
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706
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Barbosa M, Lefler FW, Berthold DE, Gettys LA, Leary JK, Laughinghouse HD. Macrophyte coverage drives microbial community structure and interactions in a shallow sub-tropical lake. Sci Total Environ 2024; 923:171414. [PMID: 38442760 DOI: 10.1016/j.scitotenv.2024.171414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/07/2024]
Abstract
Shallow lakes are typically dominated by macrophytes, which have important functional roles regulating trophic conditions and creating biological habitat. Macrophytes have been shown to strongly influence water chemistry and shape microbial communities in shallow lakes. In Florida, many large, shallow lakes are dominated by alien invasive, submersed macrophytes, such as hydrilla (Hydrilla verticillata [L.F.] Royle) and are intensively managed to reduce infestations and contain the spread of these alien invasive macrophytes. In this study, we investigated the effects of large (40 ha) herbicidal and mechanical control treatments on a large lake located in Central Florida that resulted in the reduction of Hydrilla and concomitant changes in water chemistry and microbial communities (both bacteria and protists [microbial eukaryotes]). We observed a considerable decrease in macrophyte coverage associated with plant control treatments as well as a temporal change in macrophyte coverage in Lake Tohopekaliga. We found that changes in macrophyte coverage, regardless of treatment type, significantly affected the water chemistry of the lake, resulting in a sharp increase of chlorophyll a concentration as well as an increase in turbidity with the decrease of macrophyte coverage. Moreover, the decline in macrophytes led to decreases in microbial community diversity with over-representation of phototrophic functional groups. Specifically, we observed an increase in cyanobacteria with the decrease in macrophyte coverage. Our study highlights the advantages and disadvantages of macrophyte control. Although there was an initial decrease in macrophyte coverage associated with the chemical and mechanical control of aquatic plants, after a few months, we found a considerable increase in coverage. In addition, the increase of cyanobacterial relative abundance demonstrates the possible consequences of aquatic plant control such as cyanobacterial blooms if there is a continued decline of macrophytes.
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Affiliation(s)
- Maximiliano Barbosa
- Agronomy Department, Ft. Lauderdale Research and Education Center, University of Florida, IFAS, 3205 College Avenue, Davie, FL 33314, USA
| | - Forrest W Lefler
- Agronomy Department, Ft. Lauderdale Research and Education Center, University of Florida, IFAS, 3205 College Avenue, Davie, FL 33314, USA
| | - David E Berthold
- Agronomy Department, Ft. Lauderdale Research and Education Center, University of Florida, IFAS, 3205 College Avenue, Davie, FL 33314, USA
| | - Lyn A Gettys
- Agronomy Department, Ft. Lauderdale Research and Education Center, University of Florida, IFAS, 3205 College Avenue, Davie, FL 33314, USA
| | - James K Leary
- UF/IFAS Center of Aquatic and Invasive Plants, University of Florida, 7922 NW 71 St, Gainesville, FL 32653, USA
| | - H Dail Laughinghouse
- Agronomy Department, Ft. Lauderdale Research and Education Center, University of Florida, IFAS, 3205 College Avenue, Davie, FL 33314, USA.
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Fonseca A, Kenney S, Van Syoc E, Bierly S, Dini-Andreote F, Silverman J, Boney J, Ganda E. Investigating antibiotic free feed additives for growth promotion in poultry: effects on performance and microbiota. Poult Sci 2024; 103:103604. [PMID: 38484563 PMCID: PMC10951610 DOI: 10.1016/j.psj.2024.103604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/24/2024] Open
Abstract
The poultry industry is evolving towards antibiotic-free production to meet market demands and decelerate the increasing spread of the antimicrobial resistance. The growing need for antibiotic free products has challenged producers to decrease or completely stop using antimicrobials as feed supplements in broiler diet to improve feed efficiency, growth rate, and intestinal health. Natural feed additives (e.g., probiotics and phytobiotics) are promising alternatives to substitute antimicrobial growth promoters. The goal of our study was to characterize the effects of a Probiotic and an Essential Oils blend on broilers' performance and perform a time-series analysis to describe their excreta microbiome. A total of 320 Cobb 500 (1-day-old) chicks were raised for 21 d in 32 randomly allocated cages. Treatments consisted of 4 experimental diets: a basal diet, and a basal diet mixed with an Antibiotic (bacitracin methylene disalicylate), an essential oils blend (oregano oil, rosemary, and red pepper), or a Probiotic (Bacillus subtilis). Body weight (on 1, 10, and 21d), and feed intake (10d and 21d) were recorded and feed conversion ratio was calculated. Droppings were collected daily (1-21d) to characterize broilers' excreta microbiota by targeted sequencing of the bacterial 16S rRNA gene. The Probiotic significantly improved feed conversion ratio for starter phase 1 to 10d (P = 0.03), grower phase 10 to 21d (P = 0.05), and total period 1 to 21d (P = 0.01) compared to the Antibiotic. Feed supplements did not affect alpha diversity but did impact microbial beta diversity (P < 0.01). Age also impacted microbiome turnover as differences in alpha and beta diversity were detected. Furthermore, when compared to the basal diet, the probiotic and antibiotic significantly impacted relative abundance of Bifidobacterium (log2 fold change -1.44, P = 0.03), Intestinimonas (log2 fold change 0.560, P < 0.01) and Ligilactobacillus (log2 fold change -1.600, P < 0.01). Overall, Probiotic supplementation but not essential oils supplementation positively impacted broilers' growth performance by directly causing directional shifts in broilers' excreta microbiota structure.
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Affiliation(s)
- Ana Fonseca
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA
| | - Sophia Kenney
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA
| | - Emily Van Syoc
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA; Department of Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Stephanie Bierly
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA
| | - Francisco Dini-Andreote
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA; Department of Plant Science and Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Justin Silverman
- One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA; College of Information Sciences and Technology, The Pennsylvania State University, University Park, PA, USA; Department of Statistics, The Pennsylvania State University, University Park, PA, USA; Department of Medicine, The Pennsylvania State University, University Park, PA, USA; Institute for Computational and Data Science, The Pennsylvania State University, University Park, PA, USA
| | - John Boney
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA
| | - Erika Ganda
- Department of Animal Science, The Pennsylvania State University, University Park, PA, USA; One Health Microbiome Center, The Pennsylvania State University, University Park, PA, USA.
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21
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Tokash-Peters AG, Niyonzima JD, Kayirangwa M, Muhayimana S, Tokash IW, Jabon JD, Lopez SG, Kearns PJ, Woodhams DC. Mosquito Microbiomes of Rwanda: Characterizing Mosquito Host and Microbial Communities in the Land of a Thousand Hills. Microb Ecol 2024; 87:64. [PMID: 38691215 PMCID: PMC11062966 DOI: 10.1007/s00248-024-02382-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/18/2024] [Indexed: 05/03/2024]
Abstract
Mosquitoes are a complex nuisance around the world and tropical countries bear the brunt of the burden of mosquito-borne diseases. Rwanda has had success in reducing malaria and some arboviral diseases over the last few years, but still faces challenges to elimination. By building our understanding of in situ mosquito communities in Rwanda at a disturbed, human-occupied site and at a natural, preserved site, we can build our understanding of natural mosquito microbiomes toward the goal of implementing novel microbial control methods. Here, we examined the composition of collected mosquitoes and their microbiomes at two diverse sites using Cytochrome c Oxidase I sequencing and 16S V4 high-throughput sequencing. The majority (36 of 40 species) of mosquitoes captured and characterized in this study are the first-known record of their species for Rwanda but have been characterized in other nations in East Africa. We found significant differences among mosquito genera and among species, but not between mosquito sexes or catch method. Bacteria of interest for arbovirus control, Asaia, Serratia, and Wolbachia, were found in abundance at both sites and varied greatly by species.
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Affiliation(s)
- Amanda G Tokash-Peters
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA
- Center of Excellence in Biodiversity, University of Rwanda, Huye, Rwanda
| | | | | | - Simon Muhayimana
- Center of Excellence in Biodiversity, University of Rwanda, Huye, Rwanda
| | - Ivan W Tokash
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA
| | - Jaimy D Jabon
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA
| | - Sergio G Lopez
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA
| | - Patrick J Kearns
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA
| | - Douglas C Woodhams
- College of Science and Mathematics, University of Massachusetts Boston, Boston, MA, USA.
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22
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Andriienko V, Buczek M, Meier R, Srivathsan A, Łukasik P, Kolasa MR. Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction. bioRxiv 2024:2024.04.30.591865. [PMID: 38746196 PMCID: PMC11092579 DOI: 10.1101/2024.04.30.591865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens. Methods High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals. Results We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species. Conclusion Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.
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Duperron S, Halary S, Bouly JP, Roussel T, Hugoni M, Bruto M, Oger PM, Duval C, Woo A, Jézéquel D, Ader M, Leboulanger C, Agogué H, Grossi V, Troussellier M, Bernard C. Transcriptomic insights into the dominance of two phototrophs throughout the water column of a tropical hypersaline-alkaline crater lake (Dziani Dzaha, Mayotte). Front Microbiol 2024; 15:1368523. [PMID: 38741748 PMCID: PMC11089139 DOI: 10.3389/fmicb.2024.1368523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Saline-alkaline lakes often shelter high biomasses despite challenging conditions, owing to the occurrence of highly adapted phototrophs. Dziani Dzaha (Mayotte) is one such lake characterized by the stable co-dominance of the cyanobacterium Limnospira platensis and the picoeukaryote Picocystis salinarum throughout its water column. Despite light penetrating only into the uppermost meter, the prevailing co-dominance of these species persists even in light- and oxygen-deprived zones. Here, a depth profile of phototrophs metatranscriptomes, annotated using genomic data from isolated strains, is employed to identify expression patterns of genes related to carbon processing pathways including photosynthesis, transporters and fermentation. The findings indicate a prominence of gene expression associated with photosynthesis, with a peak of expression around 1 m below the surface, although the light intensity is very low and only red and dark red wavelengths can reach it, given the very high turbidity linked to the high biomass of L. platensis. Experiments on strains confirmed that both species do grow under these wavelengths, at rates comparable to those obtained under white light. A decrease in the expression of photosynthesis-related genes was observed in L. platensis with increasing depth, whereas P. salinarum maintained a very high pool of psbA transcripts down to the deepest point as a possible adaptation against photodamage, in the absence and/or very low levels of expression of genes involved in protection. In the aphotic/anoxic zone, expression of genes involved in fermentation pathways suggests active metabolism of reserve or available dissolved carbon compounds. Overall, L. platensis seems to be adapted to the uppermost water layer, where it is probably maintained thanks to gas vesicles, as evidenced by high expression of the gvpA gene. In contrast, P. salinarum occurs at similar densities throughout the water column, with a peak in abundance and gene expression levels which suggests a better adaptation to lower light intensities. These slight differences may contribute to limited inter-specific competition, favoring stable co-dominance of these two phototrophs.
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Affiliation(s)
- Sébastien Duperron
- UMR 7245 MCAM, Muséum National d’Histoire Naturelle – CNRS, Paris, France
| | - Sébastien Halary
- UMR 7245 MCAM, Muséum National d’Histoire Naturelle – CNRS, Paris, France
| | - Jean-Pierre Bouly
- UMR 7245 MCAM, Muséum National d’Histoire Naturelle – CNRS, Paris, France
| | - Théotime Roussel
- UMR 7245 MCAM, Muséum National d’Histoire Naturelle – CNRS, Paris, France
| | - Myléne Hugoni
- Université Claude Bernard Lyon 1, CNRS, INSA de Lyon, UMR 5240 Microbiologie Adaptation et Pathogénie, University of Lyon, Villeurbanne, France
- Institut Universitaire de France, Paris, France
| | - Maxime Bruto
- Anses, UMR Mycoplasmoses Animales, VetAgro Sup, Université de Lyon, Marcy-l’Étoile, France
| | - Philippe M. Oger
- Université Claude Bernard Lyon 1, CNRS, INSA de Lyon, UMR 5240 Microbiologie Adaptation et Pathogénie, University of Lyon, Villeurbanne, France
| | - Charlotte Duval
- UMR 7245 MCAM, Muséum National d’Histoire Naturelle – CNRS, Paris, France
| | - Anthony Woo
- Pôle Analyse de Données UAR 2700 2AD, Muséum National d’Histoire Naturelle, Paris, France
| | - Didier Jézéquel
- Institut de Physique du Globe de Paris, Université de Paris Cité, CNRS, Paris, France
- UMR CARRTEL, INRAE-USMB, Thonon-les-Bains, France
| | - Magali Ader
- Institut de Physique du Globe de Paris, Université de Paris Cité, CNRS, Paris, France
- UMR CARRTEL, INRAE-USMB, Thonon-les-Bains, France
| | | | - Hélène Agogué
- Littoral Environnement et Sociétés, UMR 7266, CNRS La Rochelle Université, La Rochelle, France
| | - Vincent Grossi
- LGL-TPE, UMR 5276, CNRS, ENSL, Université Claude Bernard Lyon 1, Villeurbanne, France
| | | | - Cécile Bernard
- UMR 7245 MCAM, Muséum National d’Histoire Naturelle – CNRS, Paris, France
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Rolando JL, Kolton M, Song T, Liu Y, Pinamang P, Conrad R, Morris JT, Konstantinidis KT, Kostka JE. Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora. Nat Commun 2024; 15:3607. [PMID: 38684658 PMCID: PMC11059160 DOI: 10.1038/s41467-024-47646-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 04/09/2024] [Indexed: 05/02/2024] Open
Abstract
Heterotrophic activity, primarily driven by sulfate-reducing prokaryotes, has traditionally been linked to nitrogen fixation in the root zone of coastal marine plants, leaving the role of chemolithoautotrophy in this process unexplored. Here, we show that sulfur oxidation coupled to nitrogen fixation is a previously overlooked process providing nitrogen to coastal marine macrophytes. In this study, we recovered 239 metagenome-assembled genomes from a salt marsh dominated by the foundation plant Spartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria. Abundant sulfur-oxidizing bacteria encode and highly express genes for carbon fixation (RuBisCO), nitrogen fixation (nifHDK) and sulfur oxidation (oxidative-dsrAB), especially in roots stressed by sulfidic and reduced sediment conditions. Stressed roots exhibited the highest rates of nitrogen fixation and expression level of sulfur oxidation and sulfate reduction genes. Close relatives of marine symbionts from the Candidatus Thiodiazotropha genus contributed ~30% and ~20% of all sulfur-oxidizing dsrA and nitrogen-fixing nifK transcripts in stressed roots, respectively. Based on these findings, we propose that the symbiosis between S. alterniflora and sulfur-oxidizing bacteria is key to ecosystem functioning of coastal salt marshes.
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Affiliation(s)
- J L Rolando
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - M Kolton
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - T Song
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - Y Liu
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- The Pennsylvania State University, Department of Civil & Environmental Engineering, University Park, PA, 16802, USA
| | - P Pinamang
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - R Conrad
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
| | - J T Morris
- Belle Baruch Institute for Marine & Coastal Sciences, University of South Carolina, Columbia, SC, 29201, USA
| | - K T Konstantinidis
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA
- Georgia Institute of Technology, School of Civil and Environmental Engineering, Atlanta, GA, 30332, USA
| | - J E Kostka
- Georgia Institute of Technology, School of Biological Sciences, Atlanta, GA, 30332, USA.
- Georgia Institute of Technology, School of Earth and Atmospheric Sciences, Atlanta, GA, 30332, USA.
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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25
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Boie F, Ducey TF, Xing Y, Wang J, Rinklebe J. Field-aged rice hull biochar stimulated the methylation of mercury and altered the microbial community in a paddy soil under controlled redox condition changes. J Hazard Mater 2024; 472:134446. [PMID: 38696958 DOI: 10.1016/j.jhazmat.2024.134446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/25/2024] [Accepted: 04/25/2024] [Indexed: 05/04/2024]
Abstract
Mercury (Hg) contaminated paddy soils are hot spots for methylmercury (MeHg) which can enter the food chain via rice plants causing high risks for human health. Biochar can immobilize Hg and reduce plant uptake of MeHg. However, the effects of biochar on the microbial community and Hg (de)methylation under dynamic redox conditions in paddy soils are unclear. Therefore, we determined the microbial community in an Hg contaminated paddy soil non-treated and treated with rice hull biochar under controlled redox conditions (< 0 mV to 600 mV) using a biogeochemical microcosm system. Hg methylation exceeded demethylation in the biochar-treated soil. The aromatic hydrocarbon degraders Phenylobacterium and Novosphingobium provided electron donors stimulating Hg methylation. MeHg demethylation exceeded methylation in the non-treated soil and was associated with lower available organic matter. Actinobacteria were involved in MeHg demethylation and interlinked with nitrifying bacteria and nitrogen-fixing genus Hyphomicrobium. Microbial assemblages seem more important than single species in Hg transformation. For future directions, the demethylation potential of Hyphomicrobium assemblages and other nitrogen-fixing bacteria should be elucidated. Additionally, different organic matter inputs on paddy soils under constant and dynamic redox conditions could unravel the relationship between Hg (de)methylation, microbial carbon utilization and nitrogen cycling.
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Affiliation(s)
- Felizitas Boie
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water and Waste Management, Laboratory of Soil and Groundwater Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany
| | - Thomas F Ducey
- US Department of Agriculture, Coastal Plains Soil, Water, Plant Research Center, 2611 West Lucas Street, Florence, SC, USA
| | - Ying Xing
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water and Waste Management, Laboratory of Soil and Groundwater Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany; School of Chemistry and Materials Science, Guizhou Normal University, Guiyang 550002, PR China
| | - Jianxu Wang
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water and Waste Management, Laboratory of Soil and Groundwater Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany; State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Sciences, 550082 Guiyang, P.R. China
| | - Jörg Rinklebe
- University of Wuppertal, School of Architecture and Civil Engineering, Institute of Foundation Engineering, Water and Waste Management, Laboratory of Soil and Groundwater Management, Pauluskirchstraße 7, 42285 Wuppertal, Germany.
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Nimnoi P, Pirankham P, Srimuang K, Ruanpanun P. Insights into soil nematode diversity and bacterial community of Thai jasmine rice rhizosphere from different paddy fields in Thailand. PeerJ 2024; 12:e17289. [PMID: 38680886 PMCID: PMC11048080 DOI: 10.7717/peerj.17289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 04/02/2024] [Indexed: 05/01/2024] Open
Abstract
Globally, phytonematodes cause significant crop losses. Understanding the functions played by the plant rhizosphere soil microbiome during phytonematodes infection is crucial. This study examined the distribution of phytonematodes in the paddy fields of five provinces in Thailand, as well as determining the keystone microbial taxa in response to environmental factors that could be considered in the development of efficient biocontrol tactics in agriculture. The results demonstrated that Meloidogyne graminicola and Hirschmanniella spp. were the major and dominant phytonematodes distributed across the paddy fields of Thailand. Soil parameters (total P, Cu, Mg, and Zn) were the important factors affecting the abundance of both nematodes. Illumina next-generation sequencing demonstrated that the levels of bacterial diversity among all locations were not significantly different. The Acidobacteriota, Proteobacteria, Firmicutes, Actinobacteriota, Myxococcota, Chloroflexi, Verrucomicrobiota, Bacteroidota, Gemmatimonadota, and Desulfobacterota were the most abundant bacterial phyla observed at all sites. The number of classes of the Acidobacteriae, Clostridia, Bacilli, and Bacteroidia influenced the proportions of Hirschmanniella spp., Tylenchorhynchus spp., and free-living nematodes in the sampling dirt, whereas the number of classes of the Polyangia and Actinobacteria affected the amounts of Pratylenchus spp. in both roots and soils. Soil organic matter, N, and Mn were the main factors that influenced the structure of the bacterial community. Correlations among rhizosphere microbiota, soil nematodes, and soil properties will be informative data in considering phytonematode management in a rice production system.
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Affiliation(s)
- Pongrawee Nimnoi
- Microbiology Division, Department of Science and Bioinnovation, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen, Nakhon Pathom, Thailand
| | - Patawee Pirankham
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen, Nakhon Pathom, Thailand
| | - Kittipong Srimuang
- Prachinburi Rice Research Center, Division of Rice Research and Development, Rice Department, Ban Sang, Prachin Buri, Thailand
| | - Pornthip Ruanpanun
- Department of Plant Pathology, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen, Nakhon Pathom, Thailand
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27
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An R, Zhou X, He P, Lyu C, Wang D. Inulin mitigated antibiotic-induced intestinal microbiota dysbiosis - a comparison of different supplementation stages. Food Funct 2024. [PMID: 38644728 DOI: 10.1039/d3fo05186b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Antibiotics are unavoidable to be prescribed to subjects due to different reasons, and they decrease the relative abundance of beneficial microbes. Inulin, a fructan type of polysaccharide carbohydrate, on the contrary, could promote the growth of beneficial microbes. In this study, we investigated the effect of inulin on antibiotic-induced intestinal microbiota dysbiosis and compared their overall impact at different supplementation stages, i.e., post-antibiotic, at the time of antibiotic administration or prior to antibiotic treatment, in the C57BL/6 mice model. Although supplementation of inulin after antibiotic treatment could aid in the reconstruction of the intestinal microbial community its overall impact was limited and no remarkable differences were identified as compared to the spontaneous restoration. On the contrary, the effect of simultaneous and pre-supplementation was more remarkable. Simultaneous inulin supplementation significantly mitigated the antibiotic-induced dysbiosis based on alterations as evaluated using weighted and unweighted UniFrac distance between baseline and after treatment. Moreover, comparing the effect of simultaneous supplementation, pre-supplemented inulin further mitigated the antibiotic-induced dysbiosis, especially on the relative abundance of dominant microbes. Collectively, the current study found that the use of inulin could alleviate antibiotic-induced microbiota dysbiosis, and the best supplementation stage (overall effect as evaluated by beta diversity distance changes) was before the antibiotic treatment, then simultaneous supplementation and supplementation after the antibiotic treatment.
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Affiliation(s)
- Ran An
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
| | - Xilong Zhou
- State Key Laboratory of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co., Ltd, Shanghai, China
| | - Penglin He
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
| | - Chenang Lyu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
| | - Dapeng Wang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China.
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28
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Hill LJ, Messias CSMDA, Vilela CLS, Garritano AN, Villela HDM, do Carmo FL, Thomas T, Peixoto RS. Bacteria associated with the in hospite Symbiodiniaceae's phycosphere. iScience 2024; 27:109531. [PMID: 38585661 PMCID: PMC10995889 DOI: 10.1016/j.isci.2024.109531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 12/23/2023] [Accepted: 03/16/2024] [Indexed: 04/09/2024] Open
Abstract
Symbiotic interactions between Symbiodiniaceae and bacteria are still poorly explored, especially those in hospite. Here, we adapted a technique that allows for the enrichment of intact and metabolically active in hospite Symbiodiniaceae cells (ihSC) and their associated bacteria from the tissue of the model coral Pocillopora damicornis, using a discontinuous gradient of solution of isotonic Percoll (SIP). The ihSC were concentrated in the 50% SIP fraction, as determined by microscopy. The presence of bacteria associated with ihSC was confirmed by fluorescence in situ hybridization, while microbiome analysis indicated that bacteria of the families Halieaceae, Flavobacteriaceae, and Alcanivoraceae are significantly associated with ihSC. Extracellular vesicles that could be exuding molecules were detected on the symbiosome membranes. Our technique and data contribute to elucidate ihSC-bacteria interactions.
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Affiliation(s)
- Lilian Jorge Hill
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | | | - Caren Leite Spindola Vilela
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Alessandro N Garritano
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Helena Dias Muller Villela
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
| | - Flavia Lima do Carmo
- Laboratory of Molecular Microbial Ecology, Institute of Microbiology Paulo de Góes, Federal University of Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Raquel S. Peixoto
- Red Sea Research Center, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Kingdom of Saudi Arabia
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Wainwright BJ, Leon J, Vilela E, Hickman KJE, Caldwell J, Aimone B, Bischoff P, Ohran M, Morelli MW, Arlyza IS, Marwayana ON, Zahn G. Wallace's line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria. Environ Microbiome 2024; 19:23. [PMID: 38637894 PMCID: PMC11027274 DOI: 10.1186/s40793-024-00568-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/08/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND The processes that shape microbial biogeography are not well understood, and concepts that apply to macroorganisms, like dispersal barriers, may not affect microorganisms in the same predictable ways. To better understand how known macro-scale biogeographic processes can be applied at micro-scales, we examined seagrass associated microbiota on either side of Wallace's line to determine the influence of this cryptic dispersal boundary on the community structure of microorganisms. Communities were examined from twelve locations throughout Indonesia on either side of this theoretical line. RESULTS We found significant differences in microbial community structure on either side of this boundary (R2 = 0.09; P = 0.001), and identified seven microbial genera as differentially abundant on either side of the line, six of these were more abundant in the West, with the other more strongly associated with the East. Genera found to be differentially abundant had significantly smaller minimum cell dimensions (GLM: t923 = 59.50, P < 0.001) than the overall community. CONCLUSION Despite the assumed excellent dispersal ability of microbes, we were able to detect significant differences in community structure on either side of this cryptic biogeographic boundary. Samples from the two closest islands on opposite sides of the line, Bali and Komodo, were more different from each other than either was to its most distant island on the same side. We suggest that limited dispersal across this barrier coupled with habitat differences are primarily responsible for the patterns observed. The cryptic processes that drive macroorganism community divergence across this region may also play a role in the bigeographic patterns of microbiota.
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Affiliation(s)
- Benjamin J Wainwright
- Yale-NUS College, National University of Singapore, 16 College Avenue West, Singapore, 138527, Singapore.
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore.
| | - Josh Leon
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Ernie Vilela
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - K J E Hickman
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
| | - Jensen Caldwell
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Behlee Aimone
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Porter Bischoff
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Marissa Ohran
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Magnolia W Morelli
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
| | - Irma S Arlyza
- Research Center for Oceanography, National Research and Innovation Agency (BRIN), Jl. Pasir Putih I, Ancol Timur, Jakarta, 14430, Indonesia
| | - Onny N Marwayana
- Research Center for Ecology and Ethnobiology, National Research and Innovation Agency (BRIN), Jl. Raya Jakarta-Bogor KM 46, Cibinong, Bogor, 16911, Indonesia
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles (UCLA), 610 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | - Geoffrey Zahn
- Biology Department, Utah Valley University, 800 W University Parkway, Orem, UT, 84058, USA
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Imminger S, Meier DV, Schintlmeister A, Legin A, Schnecker J, Richter A, Gillor O, Eichorst SA, Woebken D. Survival and rapid resuscitation permit limited productivity in desert microbial communities. Nat Commun 2024; 15:3056. [PMID: 38632260 DOI: 10.1038/s41467-024-46920-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
Microbial activity in drylands tends to be confined to rare and short periods of rain. Rapid growth should be key to the maintenance of ecosystem processes in such narrow activity windows, if desiccation and rehydration cause widespread cell death due to osmotic stress. Here, simulating rain with 2H2O followed by single-cell NanoSIMS, we show that biocrust microbial communities in the Negev Desert are characterized by limited productivity, with median replication times of 6 to 19 days and restricted number of days allowing growth. Genome-resolved metatranscriptomics reveals that nearly all microbial populations resuscitate within minutes after simulated rain, independent of taxonomy, and invest their activity into repair and energy generation. Together, our data reveal a community that makes optimal use of short activity phases by fast and universal resuscitation enabling the maintenance of key ecosystem functions. We conclude that desert biocrust communities are highly adapted to surviving rapid changes in soil moisture and solute concentrations, resulting in high persistence that balances limited productivity.
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Affiliation(s)
- Stefanie Imminger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- University of Vienna, Doctoral School in Microbiology and Environmental Science, Vienna, Austria
| | - Dimitri V Meier
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Department of Ecological Microbiology, Bayreuth Center of Ecology and Environmental Research (BayCEER), University of Bayreuth, Bayreuth, Germany
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
- Large-Instrument Facility for Environmental and Isotope Mass Spectrometry, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Anton Legin
- Faculty of Chemistry, Institute of Inorganic Chemistry, University of Vienna, Vienna, Austria
| | - Jörg Schnecker
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Andreas Richter
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, Blaustein Institutes for Desert Research, Ben Gurion University of the Negev, Midreshet Ben Gurion, Israel
| | - Stephanie A Eichorst
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Dagmar Woebken
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
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Kruger BR, Sackett JD. Abiotic and biotic factors influencing small-scale corn production along a shade spectrum in arid urban agriculture settings. PLoS One 2024; 19:e0301633. [PMID: 38625854 PMCID: PMC11020971 DOI: 10.1371/journal.pone.0301633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 03/19/2024] [Indexed: 04/18/2024] Open
Abstract
Urban agriculture may be an avenue to help alleviate strain on the global production of staple crops like corn (Zea mays), but significant knowledge gaps exist regarding the optimization of staple crop production in urban settings, and especially in arid urban settings where different challenges exist for crop success. We sought to assess abiotic and biotic factors that impact sweet corn production in six arid urban agricultural plots with varying levels of shade stress, a known inhibitor of corn production. Corn successfully reached maturity in 50% of the studied plots (n = 18). Microbial richness and diversity were uniformly high in all plot soils and not indicated as a hinderance to corn production nor correlated with corn success. Multiple corn success metrics were positively correlated with average daytime light intensity (r = 0.74 to 0.84) and soil organic matter (r = 0.77 to 0.89), suggesting that these factors are critical aspects of successful corn production. In plots that did not receive optimal light exposure, exceptional soil health and morning vs afternoon sun exposure offset at least some degree of shade stress in these arid urban environments. Corn success metrics were negatively correlated with soil calcium, magnesium, sodium and sulfate (r = -0.71 to -0.90), suggesting that minimizing or mitigating the buildup of salt constituents in soils is critical for successful corn production. Optimizing staple crop production in arid urban agricultural settings supports food chain stability and social and economic security of local communities. This work suggests abiotic and biotic drivers of corn success which can be utilized for crop optimization in these environments.
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Affiliation(s)
- Brittany R. Kruger
- Division of Hydrologic Sciences, Desert Research Institute, Las Vegas, Nevada, United States of America
| | - Joshua D. Sackett
- Department of Biological Sciences, University of Cincinnati, Cincinnati, Ohio, United States of America
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Fortune J, van de Kamp J, Holmes B, Bodrossy L, Gibb K, Kaestli M. Dynamics of nitrogen genes in intertidal sediments of Darwin Harbour and their connection to N-biogeochemistry. Mar Environ Res 2024; 198:106500. [PMID: 38626627 DOI: 10.1016/j.marenvres.2024.106500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 03/29/2024] [Accepted: 04/08/2024] [Indexed: 04/18/2024]
Abstract
Microbial mediated nitrogen (N) transformation is subject to multiple controlling factors such as prevailing physical and chemical conditions, and little is known about these processes in sediments of wet-dry tropical macrotidal systems such as Darwin Harbour in North Australia. To understand key transformations, we assessed the association between the relative abundance of nitrogen cycling genes with trophic status, sediment partition and benthic nitrogen fluxes in Darwin Harbour. We analysed nitrogen cycling gene abundance using a functional gene microarray and quantitative PCRs targeting the denitrification gene (nosZ) and archaeal ammonia oxidation (AOA.1). We found a significant negative correlation between archaeal ammonia oxidation and silicate flux (P = 0.004), an indicator for diatom and benthic microalgal activity. It is suggested that the degradation of the diatomaceous organic matter generates localised anoxic conditions and inhibition of nitrification. Abundance of the nosZ gene was negatively correlated with nutrient load. The lowest nosZ gene levels were in hyper-eutrophic tidal creeks with anoxic conditions and increased levels of sulphide limiting the coupling of nitrification-denitrification (P = 0.016). Significantly higher levels of nosZ genes were measured in the surface (top 2 cm) compared to bulk sediment (top 10 cm) and there was a positive association with di-nitrogen flux (N2) in surface (P = 0.024) but not bulk sediment. This suggests that denitrifiers are most active in surficial sediment at the sediment-water interface. Elevated levels of nosZ genes also occurred in the sediments of tidal creek mouths and mudflats with these depositional zones combining the diffuse and seaward supply of nitrogen and carbon supporting denitrifiers. N-cycle molecular assays using surface sediments show promise as a rapid monitoring technique for impact assessment and measuring ecosystem function. This is particularly pertinent for tropical macrotidal systems where systematic monitoring is sparse and in many cases challenged by climatic extremes and remoteness.
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Affiliation(s)
- Julia Fortune
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia; Department of Environment, Parks and Water Security, Northern Territory Government, Australia.
| | | | | | | | - Karen Gibb
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Mirjam Kaestli
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Darwin, Northern Territory, Australia
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Maslin M, Paix B, van der Windt N, Ambo-Rappe R, Debitus C, Gaertner-Mazouni N, Ho R, de Voogd NJ. Prokaryotic communities of the French Polynesian sponge Dactylospongia metachromia display a site-specific and stable diversity during an aquaculture trial. Antonie Van Leeuwenhoek 2024; 117:65. [PMID: 38602593 PMCID: PMC11008079 DOI: 10.1007/s10482-024-01962-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Dynamics of microbiomes through time are fundamental regarding survival and resilience of their hosts when facing environmental alterations. As for marine species with commercial applications, such as marine sponges, assessing the temporal change of prokaryotic communities allows us to better consider the adaptation of sponges to aquaculture designs. The present study aims to investigate the factors shaping the microbiome of the sponge Dactylospongia metachromia, in a context of aquaculture development in French Polynesia, Rangiroa, Tuamotu archipelago. A temporal approach targeting explants collected during farming trials revealed a relative high stability of the prokaryotic diversity, meanwhile a complementary biogeographical study confirmed a spatial specificity amongst samples at different longitudinal scales. Results from this additional spatial analysis confirmed that differences in prokaryotic communities might first be explained by environmental changes (mainly temperature and salinity), while no significant effect of the host phylogeny was observed. The core community of D. metachromia is thus characterized by a high spatiotemporal constancy, which is a good prospect for the sustainable exploitation of this species towards drug development. Indeed, a microbiome stability across locations and throughout the farming process, as evidenced by our results, should go against a negative influence of sponge translocation during in situ aquaculture.
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Affiliation(s)
- Mathilde Maslin
- Univ Polynesie Française, Ifremer, ILM, IRD, EIO UMR 241, Tahiti, French Polynesia
| | - Benoît Paix
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.
| | - Niels van der Windt
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands
- Institute of Environmental Sciences (CML), Leiden University, PO Box 9518, 2300 RA, Leiden, the Netherlands
| | - Rohani Ambo-Rappe
- Faculty of Marine Science and Fisheries, Department of Marine Science, Hasanuddin University, Makassar, Indonesia
| | - Cécile Debitus
- IRD, Univ Brest, CNRS, Ifremer, LEMAR, 29280, Plouzané, France
| | | | - Raimana Ho
- Univ Polynesie Française, Ifremer, ILM, IRD, EIO UMR 241, Tahiti, French Polynesia
| | - Nicole J de Voogd
- Naturalis Biodiversity Center, PO Box 9517, 2300 RA, Leiden, the Netherlands.
- Institute of Biology (IBL), Leiden University, 2333 BE, PO Box 9505, Leiden, the Netherlands.
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Fernández-Guisuraga JM, Ansola G, Pinto R, Marcos E, Calvo L, Sáenz de Miera LE. Resistance of soil bacterial communities from montane heathland ecosystems in the Cantabrian mountains (NW Spain) to a gradient of experimental nitrogen deposition. Sci Total Environ 2024; 920:171079. [PMID: 38373460 DOI: 10.1016/j.scitotenv.2024.171079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/21/2024]
Abstract
Elevated atmospheric nitrogen (N) deposition on terrestrial ecosystems has become one of the most important drivers of microbial diversity loss on a global scale, and has been reported to alter the soil function of nutrient-poor, montane Calluna vulgaris heathlands in the context of global change. In this work we analyze for the first time the shifts of bacterial communities in response to experimental addition of N in Calluna heathlands as a simulation of atmospheric deposition. Specifically, we evaluated the effects of five N addition treatments (0, 10, 20, and 50 kg N ha-1 yr-1 for 3-years; and 56 kg N ha-1 yr-1 for 10-years) on the resistance of soil bacterial communities as determined by changes in their composition and alpha and beta diversities. The study was conducted in montane Calluna heathlands at different development stages (young and mature phases) in the southern side of the Cantabrian Mountains (NW Spain). Our results evidenced a substantial increase of long-term (10-years) N inputs on soil extractable N-NH4+, particularly in young Calluna stands. The alpha diversity of soil bacterial communities in mature Calluna stands did not show a significant response to experimental N addition, whereas it was significantly higher under long-term chronic N addition (56 kg N ha-1 yr-1 for 10-years) in young Calluna stands. These bacterial community shifts are mainly attributable to a decrease in the dominance of Acidobacteria phylum, the most representative in montane Calluna ecosystems, in favor of copiotrophic taxa such as Actinobacteria or Proteobacteria phyla, favored under increased N availability. Future research should investigate what specific ecosystem functions performed by soil bacterial communities may be sensitive to increased nitrogen depositions, which may have substantial implications for the understanding of montane Calluna ecosystems' stability.
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Affiliation(s)
- José Manuel Fernández-Guisuraga
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain; Centro de Investigação e de Tecnologias Agroambientais e Biológicas, Universidade de Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal.
| | - Gemma Ansola
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Rayo Pinto
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Elena Marcos
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Leonor Calvo
- Departamento de Biodiversidad y Gestión Ambiental, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
| | - Luis E Sáenz de Miera
- Departamento de Biología Molecular, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
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Coskun ÖK, Gomez-Saez GV, Beren M, Özcan D, Günay SD, Elkin V, Hoşgörmez H, Einsiedl F, Eisenreich W, Orsi WD. Quantifying genome-specific carbon fixation in a 750-meter deep subsurface hydrothermal microbial community. FEMS Microbiol Ecol 2024; 100:fiae062. [PMID: 38632042 DOI: 10.1093/femsec/fiae062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/16/2024] [Accepted: 04/16/2024] [Indexed: 04/19/2024] Open
Abstract
Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome-assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750-m deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon-fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10 mM. However, out of all the active carbon-fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.
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Affiliation(s)
- Ömer K Coskun
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Gonzalo V Gomez-Saez
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Murat Beren
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Doğacan Özcan
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Suna D Günay
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Viktor Elkin
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
| | - Hakan Hoşgörmez
- Department of Geological Engineering, Istanbul University - Cerrahpasa, Büyükçekmece Campus, Block G, Floor 5, Istanbul, Turkey
| | - Florian Einsiedl
- Chair of Hydrogeology, School of Engineering and Design, Technical University Munich, Arcisstraße 21, 80333 Munich, Germany
| | - Wolfgang Eisenreich
- Lehrstuhl für Biochemie, Department Chemie, Technische Universität München, Lichtenbergstraße, 85748 Garching, Germany
| | - William D Orsi
- Department of Earth and Environmental Sciences, Ludwig-Maximilians-Universität, Richard-Wagner Straße 10, 80333 Munich, Germany
- GeoBio-Center, Ludwig-Maximilians-Universität München, Richard-Wagner Straße 10, 80333 Munich, Germany
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Kaplan DI, Boyanov MI, Losey NA, Lin P, Xu C, O’Loughlin EJ, Santschi PH, Xing W, Kuhne WW, Kemner KM. Uranium Biogeochemistry in the Rhizosphere of a Contaminated Wetland. Environ Sci Technol 2024; 58:6381-6390. [PMID: 38547454 PMCID: PMC11008245 DOI: 10.1021/acs.est.3c10481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 04/10/2024]
Abstract
The objective of this study was to determine if U sediment concentrations in a U-contaminated wetland located within the Savannah River Site, South Carolina, were greater in the rhizosphere than in the nonrhizosphere. U concentrations were as much as 1100% greater in the rhizosphere than in the nonrhizosphere fractions; however and importantly, not all paired samples followed this trend. Iron (but not C, N, or S) concentrations were significantly enriched in the rhizosphere. XAS analyses showed that in both sediment fractions, U existed as UO22+ coordinated with iron(III)-oxides and organic matter. A key difference between the two sediment fractions was that a larger proportion of U was adsorbed to Fe(III)-oxides, not organic matter, in the rhizosphere, where significantly greater total Fe concentrations and greater proportions of ferrihydrite and goethite existed. Based on 16S rRNA analyses, most bacterial sequences in both paired samples were heterotrophs, and population differences were consistent with the generally more oxidizing conditions in the rhizosphere. Finally, U was very strongly bound to the whole (unfractionated) sediments, with an average desorption Kd value (Usediment/Uaqueous) of 3972 ± 1370 (mg-U/kg)/(mg-U/L). Together, these results indicate that the rhizosphere can greatly enrich U especially in wetland areas, where roots promote the formation of reactive Fe(III)-oxides.
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Affiliation(s)
- Daniel I. Kaplan
- Savannah
River Ecology Laboratory, University of
Georgia, Aiken, South Carolina 29802, United States
| | - Maxim I. Boyanov
- Argonne
National Laboratory, Lemont, Illinois 60439, United States
- Chemical
Engineering, Bulgarian Academy of Sciences, Sofia 1040, Bulgaria
| | - Nathaniel A. Losey
- Savannah
River National Laboratory, Aiken, South Carolina 29808, United States
| | - Peng Lin
- Savannah
River Ecology Laboratory, University of
Georgia, Aiken, South Carolina 29802, United States
| | - Chen Xu
- Marine
& Coastal Environmental Science, Texas
A&M University − Galveston, Galveston, Texas 77553, United States
| | | | - Peter H. Santschi
- Marine
& Coastal Environmental Science, Texas
A&M University − Galveston, Galveston, Texas 77553, United States
| | - Wei Xing
- Savannah
River Ecology Laboratory, University of
Georgia, Aiken, South Carolina 29802, United States
| | - Wendy W. Kuhne
- Savannah
River National Laboratory, Aiken, South Carolina 29808, United States
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Duan Y, Siegenthaler A, Skidmore AK, Chariton AA, Laros I, Rousseau M, De Groot GA. Forest top canopy bacterial communities are influenced by elevation and host tree traits. Environ Microbiome 2024; 19:21. [PMID: 38581032 PMCID: PMC10998314 DOI: 10.1186/s40793-024-00565-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/26/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND The phyllosphere microbiome is crucial for plant health and ecosystem functioning. While host species play a determining role in shaping the phyllosphere microbiome, host trees of the same species that are subjected to different environmental conditions can still exhibit large degrees of variation in their microbiome diversity and composition. Whether these intra-specific variations in phyllosphere microbiome diversity and composition can be observed over the broader expanse of forest landscapes remains unclear. In this study, we aim to assess the variation in the top canopy phyllosphere bacterial communities between and within host tree species in the temperate European forests, focusing on Fagus sylvatica (European beech) and Picea abies (Norway spruce). RESULTS We profiled the bacterial diversity, composition, driving factors, and discriminant taxa in the top canopy phyllosphere of 211 trees in two temperate forests, Veluwe National Parks, the Netherlands and Bavarian Forest National Park, Germany. We found the bacterial communities were primarily shaped by host species, and large variation existed within beech and spruce. While we showed that there was a core microbiome in all tree species examined, community composition varied with elevation, tree diameter at breast height, and leaf-specific traits (e.g., chlorophyll and P content). These driving factors of bacterial community composition also correlated with the relative abundance of specific bacterial families. CONCLUSIONS While our results underscored the importance of host species, we demonstrated a substantial range of variation in phyllosphere bacterial diversity and composition within a host species. Drivers of these variations have implications at both the individual host tree level, where the bacterial communities differed based on tree traits, and at the broader forest landscape level, where drivers like certain highly plastic leaf traits can potentially link forest canopy bacterial community variations to forest ecosystem processes. We eventually showed close associations between forest canopy phyllosphere bacterial communities and host trees exist, and the consistent patterns emerging from these associations are critical for host plant functioning.
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Affiliation(s)
- Yiwei Duan
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Drienerlolaan 5, PO Box 217, 7500 AE, Enschede, The Netherlands.
| | - Andjin Siegenthaler
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Drienerlolaan 5, PO Box 217, 7500 AE, Enschede, The Netherlands
| | - Andrew K Skidmore
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Drienerlolaan 5, PO Box 217, 7500 AE, Enschede, The Netherlands
| | - Anthony A Chariton
- School of Natural Sciences, Macquarie University, Sydney, NSW, Australia
| | - Ivo Laros
- Wageningen Environmental Research, Wageningen UR, P.O. Box 46, 6700 AA, Wageningen, The Netherlands
| | - Mélody Rousseau
- Faculty of Geo-Information Science and Earth Observation (ITC), University of Twente, Drienerlolaan 5, PO Box 217, 7500 AE, Enschede, The Netherlands
| | - G Arjen De Groot
- Wageningen Environmental Research, Wageningen UR, P.O. Box 46, 6700 AA, Wageningen, The Netherlands
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Yin X, Zhou G, Cai M, Richter-Heitmann T, Zhu QZ, Maeke M, Kulkarni AC, Nimzyk R, Elvert M, Friedrich MW. Physiological versatility of ANME-1 and Bathyarchaeotoa-8 archaea evidenced by inverse stable isotope labeling. Microbiome 2024; 12:68. [PMID: 38570877 PMCID: PMC10988981 DOI: 10.1186/s40168-024-01779-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 02/15/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND The trophic strategy is one key principle to categorize microbial lifestyles, by broadly classifying microorganisms based on the combination of their preferred carbon sources, electron sources, and electron sinks. Recently, a novel trophic strategy, i.e., chemoorganoautotrophy-the utilization of organic carbon as energy source but inorganic carbon as sole carbon source-has been specifically proposed for anaerobic methane oxidizing archaea (ANME-1) and Bathyarchaeota subgroup 8 (Bathy-8). RESULTS To further explore chemoorganoautotrophy, we employed stable isotope probing (SIP) of nucleic acids (rRNA or DNA) using unlabeled organic carbon and 13C-labeled dissolved inorganic carbon (DIC), i.e., inverse stable isotope labeling, in combination with metagenomics. We found that ANME-1 archaea actively incorporated 13C-DIC into RNA in the presence of methane and lepidocrocite when sulfate was absent, but assimilated organic carbon when cellulose was added to incubations without methane additions. Bathy-8 archaea assimilated 13C-DIC when lignin was amended; however, their DNA was derived from both inorganic and organic carbon sources rather than from inorganic carbon alone. Based on SIP results and supported by metagenomics, carbon transfer between catabolic and anabolic branches of metabolism is possible in these archaeal groups, indicating their anabolic versatility. CONCLUSION We provide evidence for the incorporation of the mixed organic and inorganic carbon by ANME-1 and Bathy-8 archaea in the environment. Video Abstract.
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Affiliation(s)
- Xiuran Yin
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Renmin Ave. No.58, Haikou, 570228, China.
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany.
| | - Guowei Zhou
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan University, Renmin Ave. No.58, Haikou, 570228, China
- School of Resources and Environmental Engineering, Anhui University, Hefei, Anhui, China
| | - Mingwei Cai
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
| | - Qing-Zeng Zhu
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany
| | - Mara Maeke
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany
| | - Ajinkya C Kulkarni
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
| | - Rolf Nimzyk
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
| | - Marcus Elvert
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany
- Faculty of Geosciences, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology/Chemistry, University of Bremen, James-Watt-Strasse 1, Bremen, D-28359, Germany
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Leobener Straße 8, Bremen, D-28359, Germany
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Jia Y, He C, Lahm M, Chen Q, Powers L, Gonsior M, Chen F. A pilot study suggests the correspondence between SAR202 bacteria and dissolved organic matter in the late stage of a year-long microcosm incubation. Front Microbiol 2024; 15:1357822. [PMID: 38633701 PMCID: PMC11021592 DOI: 10.3389/fmicb.2024.1357822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024] Open
Abstract
SAR202 bacteria are abundant in the marine environment and they have been suggested to contribute to the utilization of recalcitrant organic matter (RDOM) within the ocean's biogeochemical cycle. However, this functional role has only been postulated by metagenomic studies. During a one-year microcosm incubation of an open ocean microbial community with lysed Synechococcus and its released DOM, SAR202 became relatively more abundant in the later stage (after day 30) of the incubation. Network analysis illustrated a high degree of negative associations between SAR202 and a unique group of molecular formulae (MFs) in phase 2 (day 30 to 364) of the incubation, which is empirical evidence that SAR202 bacteria are major consumers of the more oxygenated, unsaturated, and higher-molecular-weight MFs. Further investigation of the SAR202-associated MFs suggested that they were potentially secondary products arising from initial heterotrophic activities following the amendment of labile Synechococcus-derived DOM. This pilot study provided a preliminary observation on the correspondence between SAR202 bacteria and more resistant DOM, further supporting the hypothesis that SAR202 bacteria play important roles in the degradation of RDOM and thus the ocean's biogeochemical cycle.
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Affiliation(s)
- Yufeng Jia
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, United States
| | - Changfei He
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Madeline Lahm
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, MD, United States
| | - Qi Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, United States
- State Key Laboratory for Marine Environmental Science, Institute of Marine Microbes and Ecospheres, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Leanne Powers
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, MD, United States
- State University of New York College of Environmental Science and Forestry, Department of Chemistry, Syracuse, NY, United States
| | - Michael Gonsior
- Chesapeake Biological Laboratory, University of Maryland Center for Environmental Science, Solomons, MD, United States
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, United States
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Brodersen KE, Mosshammer M, Bittner MJ, Hallstrøm S, Santner J, Riemann L, Kühl M. Seagrass-mediated rhizosphere redox gradients are linked with ammonium accumulation driven by diazotrophs. Microbiol Spectr 2024; 12:e0333523. [PMID: 38426746 PMCID: PMC10986515 DOI: 10.1128/spectrum.03335-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Seagrasses can enhance nutrient mobilization in their rhizosphere via complex interactions with sediment redox conditions and microbial populations. Yet, limited knowledge exists on how seagrass-derived rhizosphere dynamics affect nitrogen cycling. Using optode and gel-sampler-based chemical imaging, we show that radial O2 loss (ROL) from rhizomes and roots leads to the formation of redox gradients around below-ground tissues of seagrass (Zostera marina), which are co-localized with regions of high ammonium concentrations in the rhizosphere. Combining such chemical imaging with fine-scale sampling for microbial community and gene expression analyses indicated that multiple biogeochemical pathways and microbial players can lead to high ammonium concentration within the oxidized regions of the seagrass rhizosphere. Symbiotic N2-fixing bacteria (Bradyrhizobium) were particularly abundant and expressed the diazotroph functional marker gene nifH in Z. marina rhizosphere areas with high ammonium concentrations. Such an association between Z. marina and Bradyrhizobium can facilitate ammonium mobilization, the preferred nitrogen source for seagrasses, enhancing seagrass productivity within nitrogen-limited environments. ROL also caused strong gradients of sulfide at anoxic/oxic interfaces in rhizosphere areas, where we found enhanced nifH transcription by sulfate-reducing bacteria. Furthermore, we found a high abundance of methylotrophic and sulfide-oxidizing bacteria in rhizosphere areas, where O2 was released from seagrass rhizomes and roots. These bacteria could play a beneficial role for the plants in terms of their methane and sulfide oxidation, as well as their formation of growth factors and phytohormones. ROL from below-ground tissues of seagrass, thus, seems crucial for ammonium production in the rhizosphere via stimulation of multiple diazotrophic associations. IMPORTANCE Seagrasses are important marine habitats providing several ecosystem services in coastal waters worldwide, such as enhancing marine biodiversity and mitigating climate change through efficient carbon sequestration. Notably, the fitness of seagrasses is affected by plant-microbe interactions. However, these microscale interactions are challenging to study and large knowledge gaps prevail. Our study shows that redox microgradients in the rhizosphere of seagrass select for a unique microbial community that can enhance the ammonium availability for seagrass. We provide first experimental evidence that Rhizobia, including the symbiotic N2-fixing bacteria Bradyrhizobium, can contribute to the bacterial ammonium production in the seagrass rhizosphere. The release of O2 from rhizomes and roots also caused gradients of sulfide in rhizosphere areas with enhanced nifH transcription by sulfate-reducing bacteria. O2 release from seagrass root systems thus seems crucial for ammonium production in the rhizosphere via stimulation of multiple diazotrophic associations.
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Affiliation(s)
| | - Maria Mosshammer
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Meriel J. Bittner
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Søren Hallstrøm
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Jakob Santner
- Department of Crop Sciences, Institute of Agronomy, University of Natural Resources and Life Sciences Vienna, Tulln an der Donau, Austria
| | - Lasse Riemann
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
| | - Michael Kühl
- Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark
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Probst M, Telagathoti A, Mandolini E, Peintner U. Fungal and bacterial communities and their associations in snow-free and snow covered (sub-)alpine Pinus cembra forest soils. Environ Microbiome 2024; 19:20. [PMID: 38566162 PMCID: PMC10985912 DOI: 10.1186/s40793-024-00564-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/24/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND In Europe, Pinus cembra forests cover subalpine and alpine areas and they are of high conservational and ecological relevance. These forests experience strong seasonality with alternating snow-free and snow covered periods. Although P. cembra is known for mycorrhization and mycorrhizae usually involve fungi, plants and bacteria, the community compositions of fungi and bacteria and their associations in (sub-)alpine P. cembra forests remain vastly understudied. Here, we studied the fungal and bacterial community compositions in three independent (sub-)alpine P. cembra forests and inferred their microbial associations using marker gene sequencing and network analysis. We asked about the effect of snow cover on microbial compositions and associations. In addition, we propose inferring microbial associations across a range of filtering criteria, based on which we infer well justified, concrete microbial associations with high potential for ecological relevance that are typical for P. cembra forests and depending on snow cover. RESULTS The overall fungal and bacterial community structure was comparable with regards to both forest locations and snow cover. However, occurrence, abundance, and diversity patterns of several microbial taxa typical for P. cembra forests differed among snow-free and snow covered soils, e.g. Russula, Tetracladium and Phenoliphera. Moreover, network properties and microbial associations were influenced by snow cover. Here, we present concrete microbial associations on genus and species level that were repeatedly found across microbial networks, thereby confirming their ecological relevance. Most importantly, ectomycorrhizal fungi, such as Basidioascus, Pseudotomentella and Rhizopogon, as well as saprobic Mortierella changed their bacterial association partners depending on snow cover. CONCLUSION This is the first study researching fungal-bacterial associations across several (sub-)alpine P. cembra forests. The poorly investigated influence of snow cover on soil fungi and bacteria, especially those mycorrhizing P. cembra roots, but also saprobic soil organisms, underlines the relevance of forest seasonality. Our findings highlight that the seasonal impact of snow cover has significant consequences for the ecology of the ecosystem, particularly in relation to mycorrhization and nutrient cycling. It is imperative to consider such effects for a comprehensive understanding of the functioning resilience and responsiveness of an ecosystem.
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Affiliation(s)
- Maraike Probst
- Department for Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Anusha Telagathoti
- Department for Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Edoardo Mandolini
- Department for Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Ursula Peintner
- Department for Microbiology, Universität Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
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Lange MJ, Silva LHP, Zambom MA, Soder KJ, Brito AF. Feeding alfalfa-grass or red clover-grass mixture baleage: Effect on milk yield and composition, ruminal fermentation and microbiota taxa relative abundance, and nutrient utilization in dairy cows. J Dairy Sci 2024; 107:2066-2086. [PMID: 37863298 DOI: 10.3168/jds.2023-23836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 10/01/2023] [Indexed: 10/22/2023]
Abstract
Our goal was to investigate the effect of diets containing baleages harvested from alfalfa-grass or red clover-grass mixture on production performance, ruminal fermentation and microbiota taxa relative abundance, milk fatty acid profile, and nutrient utilization in dairy cows. Twenty Jersey cows (18 multiparous and 2 primiparous) averaging (mean ± SD) 148 ± 45.2 days in milk and 483 ± 65.4 kg of body weight in the beginning of the study were used in a randomized complete block design with repeated measures over time. The experiment lasted 9 wk, with a 2 wk covariate period followed by 7 wk of data and sample collection (wk 4 and 7 used in the statistical analyses). Cows were fed diets containing (dry matter basis) 35% of a concentrate mash and the following forage sources: (1) 65% second- and third-cut (32.5% each) alfalfa-grass mixture baleages (ALF) or (2) 65% second- and third-cut (32.5% each) red clover-grass mixture baleages (RC). Diets did not affect dry matter intake, milk yield, and concentrations of milk fat and true protein. In contrast, milk fat yield tended to decrease and energy-corrected milk yield decreased with feeding RC versus ALF. The apparent total-tract digestibilities of dry matter, organic matter, and ash-free neutral detergent fiber, milk proportions of trans-10 18:1, cis-9,cis-12,cis-15 18:3, and total n-3 fatty acids, ruminal molar proportion of acetate, and plasma concentrations of Leu, Phe, and Val all increased in RC versus ALF. Diet × week interactions were found for several parameters, most notably ruminal molar proportions of propionate and butyrate, ruminal NH3-N, milk urea N, plasma urea N, and plasma His concentrations, urinary N excretion, enteric CH4 production, and all energy efficiency variables. Specifically, ruminal NH3-N and plasma urea N concentrations, urinary excretion of N, and CH4 production decreased in cows fed RC in wk 4 but not in wk 7. Milk urea N concentration decreased and that of plasma His increased with feeding RC during wk 4 and 7, although the magnitude of treatments difference varied between the sampling periods. Efficiency of energy utilization calculated as milk energy/metabolizable energy decreased and that of tissue energy/ME increased in RC versus ALF cows in wk 4, suggesting that ME was portioned toward tissue and not milk in the RC diet. Interactions were also observed for the relative abundance of the rumen bacterial phyla Verrucomicrobiota and Fibrobacterota, with cows offered RC showing greater values than those receiving ALF in wk 4 but no differences in wk 7. Several diet × week interactions were detected in the present study implying short-term treatment responses and warranting further investigations.
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Affiliation(s)
- M J Lange
- Universidade Estadual do Oeste do Paraná, Marechal Cândido Rondon, Paraná, Brazil 85960-000
| | - L H P Silva
- Department of Agriculture, Nutrition and Food Systems, University of New Hampshire, Durham, NH 03824
| | - M A Zambom
- Universidade Estadual do Oeste do Paraná, Marechal Cândido Rondon, Paraná, Brazil 85960-000
| | - K J Soder
- Pasture Systems and Watershed Management Research Unit, USDA-Agricultural Research Service, University Park, PA 16802-3702
| | - A F Brito
- Department of Agriculture, Nutrition and Food Systems, University of New Hampshire, Durham, NH 03824.
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Reignier O, Bormans M, Hervé F, Robert E, Savar V, Tanniou S, Amzil Z, Noël C, Briand E. Spatio-temporal connectivity of a toxic cyanobacterial community and its associated microbiome along a freshwater-marine continuum. Harmful Algae 2024; 134:102627. [PMID: 38705620 DOI: 10.1016/j.hal.2024.102627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/22/2024] [Accepted: 04/10/2024] [Indexed: 05/07/2024]
Abstract
Due to climate changes and eutrophication, blooms of predominantly toxic freshwater cyanobacteria are intensifying and are likely to colonize estuaries, thus impacting benthic organisms and shellfish farming representing a major ecological, health and economic risk. In the natural environment, Microcystis form large mucilaginous colonies that influence the development of both cyanobacterial and embedded bacterial communities. However, little is known about the fate of natural colonies of Microcystis by salinity increase. In this study, we monitored the fate of a Microcystis dominated bloom and its microbiome along a French freshwater-marine gradient at different phases of a bloom. We demonstrated changes in the cyanobacterial genotypic composition, in the production of specific metabolites (toxins and compatible solutes) and in the heterotrophic bacteria structure in response to the salinity increase. In particular M. aeruginosa and M. wesenbergii survived salinities up to 20. Based on microcystin gene abundance, the cyanobacteria became more toxic during their estuarine transfer but with no selection of specific microcystin variants. An increase in compatible solutes occurred along the continuum with extensive trehalose and betaine accumulations. Salinity structured most the heterotrophic bacteria community, with an increased in the richness and diversity along the continuum. A core microbiome in the mucilage-associated attached fraction was highly abundant suggesting a strong interaction between Microcystis and its microbiome and a likely protecting role of the mucilage against an osmotic shock. These results underline the need to better determine the interactions between the Microcystis colonies and their microbiome as a likely key to their widespread success and adaptation to various environmental conditions.
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Affiliation(s)
| | - Myriam Bormans
- UMR CNRS 6553 ECOBIO, University of Rennes 1, Rennes F-35042, France
| | - Fabienne Hervé
- IFREMER, PHYTOX, Laboratoire METALG, Nantes F-44000, France
| | - Elise Robert
- IFREMER, PHYTOX, Laboratoire GENALG, Nantes F-44000, France
| | | | - Simon Tanniou
- IFREMER, PHYTOX, Laboratoire METALG, Nantes F-44000, France
| | - Zouher Amzil
- IFREMER, PHYTOX, Laboratoire METALG, Nantes F-44000, France
| | - Cyril Noël
- IFREMER, IRSI - Service de Bioinformatique (SeBiMER), Plouzané, France
| | - Enora Briand
- IFREMER, PHYTOX, Laboratoire GENALG, Nantes F-44000, France.
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Yan Y, Lee J, Han IL, Wang Z, Li G, McCullough K, Klaus S, Kang D, Wang D, Patel A, McQuarrie J, Stinson BM, deBarbadillo C, Dombrowski P, Bott C, Gu AZ. Comammox and unknown ammonia oxidizers contribute to nitrite accumulation in an integrated A-B stage process that incorporates side-stream EBPR (S2EBPR). Water Res 2024; 253:121220. [PMID: 38341969 DOI: 10.1016/j.watres.2024.121220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/27/2023] [Accepted: 01/28/2024] [Indexed: 02/13/2024]
Abstract
A novel integrated pilot-scale A-stage high rate activated sludge, B-stage short-cut biological nitrogen removal and side-stream enhanced biological phosphorus removal (A/B-shortcut N-S2EBPR) process for treating municipal wastewater was demonstrated with the aim to achieve simultaneous and carbon- and energy-efficient N and P removal. In this studied period, an average of 7.62 ± 2.17 mg-N/L nitrite accumulation was achieved through atypical partial nitrification without canonical known NOB out-selection. Network analysis confirms the central hub of microbial community as Nitrospira, which was one to two orders of magnitude higher than canonical aerobic oxidizing bacteria (AOB) in a B-stage nitrification tank. The contribution of comammox Nitrospira as AOB was evidenced by the increased amoB/nxr ratio and higher ammonia oxidation activity. Furthermore, oligotyping analysis of Nitrospira revealed two dominant sub-clusters (microdiveristy) within the Nitrospira. The relative abundance of oligotype II, which is phylogenetically close to Nitrospira_midas_s_31566, exhibited a positive correlation with nitrite accumulation in the same operational period, suggesting its role as comammox Nitrospira. Additionally, the phylogenetic investigation suggested that heterotrophic organisms from the family Comamonadacea and the order Rhodocyclaceae embedding ammonia monooxygenase and hydroxylamine oxidase may function as heterotrophic nitrifiers. This is the first study that elucidated the impact of integrating the S2EBPR on nitrifying populations with implications on short-cut N removal. The unique conditions in the side-stream reactor, such as low ORP, favorable VFA concentrations and composition, seemed to exert different selective forces on nitrifying populations from those in conventional biological nutrient removal processes. The results provide new insights for integrating EBPR with short-cut N removal process for mainstream wastewater treatment.
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Affiliation(s)
- Yuan Yan
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States
| | - Jangho Lee
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States
| | - I L Han
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States
| | - Zijian Wang
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States
| | - Guangyu Li
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States
| | - Kester McCullough
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States; Hampton Roads Sanitation District, Virginia Beach, VA 23454, United States; modelEAU, Département de génie civil et de génie des eaux, Université Laval, 1065 av. de la Médecine, Québec, Canada
| | - Stephanie Klaus
- Hampton Roads Sanitation District, Virginia Beach, VA 23454, United States
| | - Da Kang
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States; Department of Environmental Engineering, College of Environmental & Resource Sciences, Zhejiang University, China
| | - Dongqi Wang
- Department of Municipal and Environmental Engineering, Xi'an University of Technology, Xi'an, Shaanxi 710048, China; Department of Civil and Environmental Engineering, Northeastern University, Boston, MA 02115, United States
| | - Anand Patel
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States
| | - Jim McQuarrie
- Denver Metro Wastewater Reclamation District, Denver, CO 80229, United States
| | | | - Christine deBarbadillo
- District of Columbia Water and Sewer Authority, District of Columbia, 5000 Overlook Ave., SW, Washington, DC 20032, United States
| | | | - Charles Bott
- Hampton Roads Sanitation District, Virginia Beach, VA 23454, United States.
| | - April Z Gu
- School of Civil and Environmental Engineering, Cornell University, Ithaca, NY 14850, United States.
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Horstmann L, Lipus D, Bartholomäus A, Arens F, Airo A, Ganzert L, Zamorano P, Schulze-Makuch D, Wagner D. Persistent microbial communities in hyperarid subsurface habitats of the Atacama Desert: Insights from intracellular DNA analysis. PNAS Nexus 2024; 3:pgae123. [PMID: 38655503 PMCID: PMC11037274 DOI: 10.1093/pnasnexus/pgae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
Desert environments constitute one of the largest and yet most fragile ecosystems on Earth. Under the absence of regular precipitation, microorganisms are the main ecological component mediating nutrient fluxes by using soil components, like minerals and salts, and atmospheric gases as a source for energy and water. While most of the previous studies on microbial ecology of desert environments have focused on surface environments, little is known about microbial life in deeper sediment layers. Our study is extending the limited knowledge about microbial communities within the deeper subsurface of the hyperarid core of the Atacama Desert. By employing intracellular DNA extraction and subsequent 16S rRNA sequencing of samples collected from a soil pit in the Yungay region of the Atacama Desert, we unveiled a potentially viable microbial subsurface community residing at depths down to 4.20 m. In the upper 80 cm of the playa sediments, microbial communities were dominated by Firmicutes taxa showing a depth-related decrease in biomass correlating with increasing amounts of soluble salts. High salt concentrations are possibly causing microbial colonization to cease in the lower part of the playa sediments between 80 and 200 cm depth. In the underlying alluvial fan deposits, microbial communities reemerge, possibly due to gypsum providing an alternative water source. The discovery of this deeper subsurface community is reshaping our understanding of desert soils, emphasizing the need to consider subsurface environments in future explorations of arid ecosystems.
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Affiliation(s)
- Lucas Horstmann
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
- Department Experimental Phycology and Culture Collection of Algae (EPSAG), Albrecht-von-Haller-Institute for Plant Sciences, Georg August University Göttingen, 37073 Göttingen, Germany
| | - Daniel Lipus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Alexander Bartholomäus
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
| | - Felix Arens
- Zentrum für Astronomie und Astrophysik, Technische Universität Berlin, 10623 Berlin, Germany
| | - Alessandro Airo
- Museum für Naturkunde, Leibniz-Institut für Evolutions- und Biodiversitätsforschung, 10115 Berlin, Germany
| | - Lars Ganzert
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 16775 Stechlin, Germany
| | - Pedro Zamorano
- Laboratorio de Microorganismos Extremófilos, University of Antofagasta, Antofagasta 02800, Chile
| | - Dirk Schulze-Makuch
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
- Zentrum für Astronomie und Astrophysik, Technische Universität Berlin, 10623 Berlin, Germany
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, 16775 Stechlin, Germany
| | - Dirk Wagner
- GFZ German Research Centre for Geosciences, Section Geomicrobiology, 14473 Potsdam, Germany
- Institute of Geosciences, University of Potsdam, 14476 Potsdam, Germany
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Rassner SME, Cook JM, Mitchell AC, Stevens IT, Irvine-Fynn TDL, Hodson AJ, Edwards A. The distinctive weathering crust habitat of a High Arctic glacier comprises discrete microbial micro-habitats. Environ Microbiol 2024; 26:e16617. [PMID: 38558266 DOI: 10.1111/1462-2920.16617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/08/2024] [Indexed: 04/04/2024]
Abstract
Sunlight penetrates the ice surfaces of glaciers and ice sheets, forming a water-bearing porous ice matrix known as the weathering crust. This crust is home to a significant microbial community. Despite the potential implications of microbial processes in the weathering crust for glacial melting, biogeochemical cycles, and downstream ecosystems, there have been few explorations of its microbial communities. In our study, we used 16S rRNA gene sequencing and shotgun metagenomics of a Svalbard glacier surface catchment to characterise the microbial communities within the weathering crust, their origins and destinies, and the functional potential of the weathering crust metagenome. Our findings reveal that the bacterial community in the weathering crust is distinct from those in upstream and downstream habitats. However, it comprises two separate micro-habitats, each with different taxa and functional categories. The interstitial porewater is dominated by Polaromonas, influenced by the transfer of snowmelt, and exported via meltwater channels. In contrast, the ice matrix is dominated by Hymenobacter, and its metagenome exhibits a diverse range of functional adaptations. Given that the global weathering crust area and the subsequent release of microbes from it are strongly responsive to climate projections for the rest of the century, our results underscore the pressing need to integrate the microbiome of the weathering crust with other communities and processes in glacial ecosystems.
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Affiliation(s)
| | - Joseph M Cook
- Department of Life Sciences, Aberystwyth University, Wales, UK
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
| | - Andrew C Mitchell
- Department of Geography and Earth Sciences, Aberystwyth University, Wales, UK
| | - Ian T Stevens
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
- Department of Geography and Earth Sciences, Aberystwyth University, Wales, UK
| | | | - Andrew J Hodson
- Department of Arctic Geology, University Centre in Svalbard (UNIS), Longyearbyen, Norway
| | - Arwyn Edwards
- Department of Life Sciences, Aberystwyth University, Wales, UK
- Department of Arctic Biology, University Centre in Svalbard (UNIS), Longyearbyen, Norway
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47
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An R, Zhou X, Zhang J, Yang Y, Lyu C, Wang D. Restoration of Intestinal Microbiota After Inulin Supplementation Halted: The Secondary Effect of Supplemented Inulin. Mol Nutr Food Res 2024; 68:e2400033. [PMID: 38483096 DOI: 10.1002/mnfr.202400033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/19/2024] [Indexed: 04/17/2024]
Abstract
SCOPE Consumption of inulin could affect the intestinal microbiota composition. Hereby, it is aimed to investigate the intestinal microbial community restoration process when the inulin supplementation is terminated (i.e., the secondary effect). METHODS AND RESULTS The current study investigates the response and restoration of intestinal microbiota to/after high (Inulin-H) and low (Inulin-L) dosage of inulin supplementation or sequential antibiotics and inulin (Anti-Inulin-L) supplementation, based on analysis of 16S rRNA gene sequences in C57BL/6 mice. The number of significantly changed genera in response to inulin is highest in Anti-Inulin-L (n = 66) group, followed by Inulin-H (n = 51) and Inulin-L (n = 38) group. After inulin supplementation stops, microbiota of all studied groups tend to recover to their original states, with highest percentage of inulin-responding microbes stay significantly different at Anti-Inulin-L (93.94%) group, followed by Inulin-H (74.51%) and Inulin-L (44.12%) groups. Of note, the relative abundance of some non-inulin-responding taxa significantly increases during restoration. CONCLUSION Sequential antibiotics and inulin supplementation induce greatest changes in the intestinal microbial composition, followed by high and low dosage of inulin. Additionally, the changes induce by supplemented inulin in the intestinal microbial community, provide a chance for some microbes to outcompete the other microbes during the spontaneous restoration.
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Affiliation(s)
- Ran An
- School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan 800, Shanghai, 200240, China
| | - Xilong Zhou
- State Key Laboratory of Dairy Biotechnology, Dairy Research Institute, Bright Dairy and Food Co., Ltd, Shanghai, China, Jiangchang West Road 1518, Shanghai, 200436, China
| | - Jing Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan 800, Shanghai, 200240, China
| | - Yaqi Yang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan 800, Shanghai, 200240, China
| | - Chengang Lyu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan 800, Shanghai, 200240, China
| | - Dapeng Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Dongchuan 800, Shanghai, 200240, China
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48
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Becker CC, Weber L, Llopiz JK, Mooney TA, Apprill A. Microorganisms uniquely capture and predict stony coral tissue loss disease and hurricane disturbance impacts on US Virgin Island reefs. Environ Microbiol 2024; 26:e16610. [PMID: 38576217 DOI: 10.1111/1462-2920.16610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 03/01/2024] [Indexed: 04/06/2024]
Abstract
Coral reef ecosystems are now commonly affected by major climate and disease disturbances. Disturbance impacts are typically recorded using reef benthic cover, but this may be less reflective of other ecosystem processes. To explore the potential for reef water-based disturbance indicators, we conducted a 7-year time series on US Virgin Island reefs where we examined benthic cover and reef water nutrients and microorganisms from 2016 to 2022, which included two major disturbances: hurricanes Irma and Maria in 2017 and the stony coral tissue loss disease outbreak starting in 2020. The disease outbreak coincided with the largest changes in the benthic habitat, with increases in the percent cover of turf algae and Ramicrusta, an invasive alga. While sampling timepoint contributed most to changes in reef water nutrient composition and microbial community beta diversity, both disturbances led to increases in ammonium concentration, a mechanism likely contributing to observed microbial community shifts. We identified 10 microbial taxa that were sensitive and predictive of increasing ammonium concentration. This included the decline of the oligotrophic and photoautotrophic Prochlorococcus and the enrichment of heterotrophic taxa. As disturbances impact reefs, the changing nutrient and microbial regimes may foster a type of microbialization, a process that hastens reef degradation.
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Affiliation(s)
- Cynthia C Becker
- MIT-WHOI Joint Program in Oceanography/Applied Ocean Science and Engineering, Cambridge and Woods Hole, Massachusetts, USA
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Laura Weber
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Joel K Llopiz
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - T Aran Mooney
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | - Amy Apprill
- Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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49
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Hellman M, Juhanson J, Wallnäs F, Herbert RB, Hallin S. Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures. J Environ Manage 2024; 356:120607. [PMID: 38537471 DOI: 10.1016/j.jenvman.2024.120607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/08/2024] [Accepted: 03/10/2024] [Indexed: 04/07/2024]
Abstract
Mining activities are increasingly recognized for contributing to nitrogen (N) pollution and possibly also to emissions of the greenhouse gas nitrous oxide (N2O) due to undetonated, N-based explosives. A woodchip denitrifying bioreactor, installed to treat nitrate-rich leachate from waste rock dumps in northern Sweden, was monitored for two years to determine the spatial and temporal distribution of microbial communities, including the genetic potential for different N transformation processes, in pore water and woodchips and how this related to reactor N removal capacity. About 80 and 65 % of the nitrate was removed during the first and second operational year, respectively. There was a succession in the microbial community over time and in space along the reactor length in both pore water and woodchips, which was reflected in reactor performance. Nitrate ammonification likely had minimal impact on N removal efficiency due to the low production of ammonium and low abundance of the key gene nrfA in ammonifiers. Nitrite and N2O were formed in the bioreactor and released in the effluent water, although direct N2O emissions from the surface was low. That these unwanted reactive N species were produced at different times and locations in the reactor indicate that the denitrification pathway was temporally as well as spatially separated along the reactor length. We conclude that the succession of microbial communities in woodchip denitrifying bioreactors treating mining water develops slowly at low temperature, which impacts reactor performance.
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Affiliation(s)
- Maria Hellman
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 75007, Uppsala, Sweden.
| | - Jaanis Juhanson
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 75007, Uppsala, Sweden.
| | - Felicia Wallnäs
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 75007, Uppsala, Sweden.
| | - Roger B Herbert
- Uppsala University, Department of Earth Sciences, Villavägen 16, 75226, Uppsala, Sweden.
| | - Sara Hallin
- Swedish University of Agricultural Sciences, Department of Forest Mycology and Plant Pathology, Box 7026, 75007, Uppsala, Sweden.
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50
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Edwards JD, Krichels AH, Seyfried GS, Dalling J, Kent AD, Yang WH. Soil microbial community response to ectomycorrhizal dominance in diverse neotropical montane forests. Mycorrhiza 2024; 34:95-105. [PMID: 38183463 PMCID: PMC10998807 DOI: 10.1007/s00572-023-01134-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024]
Abstract
Ectomycorrhizal (EM) associations can promote the dominance of tree species in otherwise diverse tropical forests. These EM associations between trees and their fungal mutualists have important consequences for soil organic matter cycling, yet the influence of these EM-associated effects on surrounding microbial communities is not well known, particularly in neotropical forests. We examined fungal and prokaryotic community composition in surface soil samples from mixed arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) stands as well as stands dominated by EM-associated Oreomunnea mexicana (Juglandaceae) in four watersheds differing in soil fertility in the Fortuna Forest Reserve, Panama. We hypothesized that EM-dominated stands would support distinct microbial community assemblages relative to the mixed AM-EM stands due to differences in carbon and nitrogen cycling associated with the dominance of EM trees. We expected that this microbiome selection in EM-dominated stands would lead to lower overall microbial community diversity and turnover, with tighter correspondence between general fungal and prokaryotic communities. We measured fungal and prokaryotic community composition via high-throughput Illumina sequencing of the ITS2 (fungi) and 16S rRNA (prokaryotic) gene regions. We analyzed differences in alpha and beta diversity between forest stands associated with different mycorrhizal types, as well as the relative abundance of fungal functional groups and various microbial taxa. We found that fungal and prokaryotic community composition differed based on stand mycorrhizal type. There was lower prokaryotic diversity and lower relative abundance of fungal saprotrophs and pathogens in EM-dominated than AM-EM mixed stands. However, contrary to our prediction, there was lower homogeneity for fungal communities in EM-dominated stands compared to mixed AM-EM stands. Overall, we demonstrate that EM-dominated tropical forest stands have distinct soil microbiomes relative to surrounding diverse forests, suggesting that EM fungi may filter microbial functional groups in ways that could potentially influence plant performance or ecosystem function.
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Affiliation(s)
- Joseph D Edwards
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA.
| | - Alexander H Krichels
- USDA Forest Service, Rocky Mountain Research Station, Albuquerque, NM, 87102, USA
| | - Georgia S Seyfried
- Department of Forest Ecology and Resource Management, Oregon State University, Corvallis, OR, 97331, USA
| | - James Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Angela D Kent
- Department of Natural Resources and Environmental Science, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Wendy H Yang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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