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Cunha IDCMD, Silva AVRD, Boleta EHM, Pellegrinetti TA, Zagatto LFG, Zagatto SDSS, Chaves MGD, Mendes R, Patreze CM, Tsai SM, Mendes LW. The interplay between the inoculation of plant growth-promoting rhizobacteria and the rhizosphere microbiome and their impact on plant phenotype. Microbiol Res 2024; 283:127706. [PMID: 38574431 DOI: 10.1016/j.micres.2024.127706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/06/2024]
Abstract
Microbial inoculation stands as a pivotal strategy, fostering symbiotic relationships between beneficial microorganisms and plants, thereby enhancing nutrient uptake, bolstering resilience against environmental stressors, and ultimately promoting healthier and more productive plant growth. However, while the advantageous roles of inoculants are widely acknowledged, the precise and nuanced impacts of inoculation on the intricate interactions of the rhizosphere microbiome remain significantly underexplored. This study explores the impact of bacterial inoculation on soil properties, plant growth, and the rhizosphere microbiome. By employing various bacterial strains and a synthetic community (SynCom) as inoculants in common bean plants, the bacterial and fungal communities in the rhizosphere were assessed through 16 S rRNA and ITS gene sequencing. Concurrently, soil chemical parameters, plant traits, and gene expression were evaluated. The findings revealed that bacterial inoculation generally decreased pH and V%, while increasing H+Al and m% in the rhizosphere. It also decreased gene expression in plants related to detoxification, photosynthesis, and defense mechanisms, while enhancing bacterial diversity in the rhizosphere, potentially benefiting plant health. Specific bacterial strains showed varied impacts on rhizosphere microbiome assembly, predominantly affecting rhizospheric bacteria more than fungi, indirectly influencing soil conditions and plants. Notably, Paenibacillus polymyxa inoculation improved plant nitrogen (by 5.2%) and iron levels (by 28.1%), whereas Bacillus cereus boosted mycorrhization rates (by 70%). Additionally, inoculation led to increased complexity in network interactions within the rhizosphere (∼15%), potentially impacting plant health. Overall, the findings highlight the significant impact of introducing bacteria to the rhizosphere, enhancing nutrient availability, microbial diversity, and fostering beneficial plant-microbe interactions.
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Affiliation(s)
- Izadora de Cássia Mesquita da Cunha
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil; Luiz de Queiroz College of Agriculture ESALQ, University of São Paulo USP, Piracicaba, SP 13418-900, Brazil
| | - Ana Vitória Reina da Silva
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Eduardo Henrique Marcandalli Boleta
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Thierry Alexandre Pellegrinetti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Luis Felipe Guandalin Zagatto
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil; Department of Terrestrial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen NL-6700 AB, the Netherlands
| | - Solange Dos Santos Silva Zagatto
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Miriam Gonçalves de Chaves
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Rodrigo Mendes
- Laboratory of Environmental Microbiology, Embrapa Environment, Jaguariuna 18020-000, Brazil
| | - Camila Maistro Patreze
- Institute of Biosciences, Federal University of the State of Rio de Janeiro, Rio de Janeiro, RJ 22290-240, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture CENA, University of Sao Paulo USP, Piracicaba, SP 13416-000, Brazil.
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2
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Li S, Yan X, Abdullah Al M, Ren K, Rensing C, Hu A, Tsyganov AN, Mazei Y, Smirnov A, Mazei N, Yang J. Ecological and evolutionary processes involved in shaping microbial habitat generalists and specialists in urban park ecosystems. mSystems 2024:e0046924. [PMID: 38767347 DOI: 10.1128/msystems.00469-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Accepted: 04/17/2024] [Indexed: 05/22/2024] Open
Abstract
Microbiomes are integral to ecological health and human well-being; however, their ecological and evolutionary drivers have not been systematically investigated, especially in urban park ecosystems. As microbes have different levels of tolerance to environmental changes and habitat preferences, they can be categorized into habitat generalists and specialists. Here, we explored the ecological and evolutionary characteristics of both prokaryotic and microeukaryotic habitat generalists and specialists from six urban parks across five habitat types, including moss, soil, tree hole, water, and sediment. Our results revealed that different ecological and evolutionary processes maintained and regulated microbial diversity in urban park ecosystems. Under ecological perspective, community assembly of microbial communities was mainly driven by stochastic processes; however, deterministic processes were higher for habitat specialists than generalists. Microbial interactions were highly dynamic among habitats, and habitat specialists played key roles as module hubs in intradomain networks. In aquatic interdomain networks, microeukaryotic habitat specialists and prokaryotic habitat specialists played crucial roles as module hubs and connectors, respectively. Furthermore, analyzing evolutionary characteristics, our results revealed that habitat specialists had a much higher diversification potential than generalists, while generalists showed shorter phylogenetic branch lengths as well as larger genomes than specialists. This study broadens our understanding of the ecological and evolutionary features of microbial habitat generalists and specialists in urban park ecosystems across multi-habitat. IMPORTANCE Urban parks, as an important urban greenspace, play essential roles in ecosystem services and are important hotspots for microbes. Microbial diversity is driven by different ecological and evolutionary processes, while little is currently known about the distinct roles of ecological and evolutionary features in shaping microbial diversity in urban park ecosystems. We explored the ecological and evolutionary characteristics of prokaryotic and microeukaryotic habitat generalists and specialists in urban park ecosystems based on a representative set of different habitats. We found that different ecological and evolutionary drivers jointly maintained and regulated microbial diversity in urban park microbiomes through analyzing the community assembly process, ecological roles in hierarchical interaction, and species diversification potential. These findings significantly advance our understanding regarding the mechanisms governing microbial diversity in urban park ecosystems.
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Affiliation(s)
- Shuzhen Li
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Xue Yan
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mamun Abdullah Al
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Kexin Ren
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Christopher Rensing
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- Institute of Environmental Microbiology, College of Resources and the Environment, Fujian Agriculture & Forestry University, Fuzhou, China
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | | | - Yuri Mazei
- Lomonosov Moscow State University, Moscow, Russia
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, China
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences, Moscow, Russia
| | - Alexey Smirnov
- Department of Invertebrate Zoology, Faculty of Biolog, St. Petersburg University, St Petersburg, Russia
| | | | - Jun Yang
- Aquatic EcoHealth Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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3
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Richards SC, King WL, Sutherland JL, Bell TH. Leveraging aquatic-terrestrial interfaces to capture putative habitat generalists. FEMS Microbiol Lett 2024; 371:fnae025. [PMID: 38553956 DOI: 10.1093/femsle/fnae025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 02/03/2024] [Accepted: 03/28/2024] [Indexed: 04/21/2024] Open
Abstract
Habitat type is a strong determinant of microbial composition. Habitat interfaces, such as the boundary between aquatic and terrestrial systems, present unique combinations of abiotic factors for microorganisms to contend with. Aside from the spillover of certain harmful microorganisms from agricultural soils into water (e.g. fecal coliform bacteria), we know little about the extent of soil-water habitat switching across microbial taxa. In this study, we developed a proof-of-concept system to facilitate the capture of putatively generalist microorganisms that can colonize and persist in both soil and river water. We aimed to examine the phylogenetic breadth of putative habitat switchers and how this varies across different source environments. Microbial composition was primarily driven by recipient environment type, with the strongest phylogenetic signal seen at the order level for river water colonizers. We also identified more microorganisms colonizing river water when soil was collected from a habitat interface (i.e. soil at the side of an intermittently flooded river, compared to soil collected further from water sources), suggesting that environmental interfaces could be important reservoirs of microbial habitat generalists. Continued development of experimental systems that actively capture microorganisms that thrive in divergent habitats could serve as a powerful tool for identifying and assessing the ecological distribution of microbial generalists.
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Affiliation(s)
- Sarah C Richards
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, United States
- Department of Ecosystem Science and Management, The Pennsylvania State University, University Park, PA, 16802, United States
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, United States
- International Agriculture and Development Graduate Program, The Pennsylvania State University, University Park, PA, 16802, United States
| | - William L King
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, United States
- School of Biological Sciences, University of Southampton, SO17 1BJ, United Kingdom
| | - Jeremy L Sutherland
- Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, United States
| | - Terrence H Bell
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, PA, 16802, United States
- Intercollege Graduate Degree Program in Ecology, The Pennsylvania State University, University Park, PA, 16802, United States
- International Agriculture and Development Graduate Program, The Pennsylvania State University, University Park, PA, 16802, United States
- Department of Physical & Environmental Sciences, University of Toronto Scarborough, Toronto, ON, M1C1A4, Canada
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4
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Zhao J, Huang L, Chakrabarti S, Cooper J, Choi E, Ganan C, Tolchinsky B, Triplett EW, Daroub SH, Martens-Habbena W. Nitrogen and phosphorous acquisition strategies drive coexistence patterns among archaeal lineages in soil. THE ISME JOURNAL 2023; 17:1839-1850. [PMID: 37596409 PMCID: PMC10579303 DOI: 10.1038/s41396-023-01493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/06/2023] [Accepted: 08/08/2023] [Indexed: 08/20/2023]
Abstract
Soil represents the largest reservoir of Archaea on Earth. Present-day archaeal diversity in soils globally is dominated by members of the class Nitrososphaeria. The evolutionary radiation of this class is thought to reflect adaptations to a wide range of temperatures, pH, and other environmental conditions. However, the mechanisms that govern competition and coexistence among Nitrososphaeria lineages in soil remain poorly understood. Here we show that predominant soil Nitrososphaeria lineages compose a patchwork of gene inventory and expression profiles for ammonia, urea, and phosphate utilization. In contrast, carbon fixation, respiration, and ATP synthesis genes are conserved and expressed consistently among predominant phylotypes across 12 major evolutionary lineages commonly found in soil. In situ gene expression profiles closely resemble pure culture reference strains under optimal growth conditions. Together, these results reveal resource-based coexistence patterns among Nitrososphaeria lineages and suggest complementary ecophysiological niches associated with differential nutrient acquisition strategies among globally predominant archaeal lineages in soil.
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Affiliation(s)
- Jun Zhao
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Laibin Huang
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Seemanti Chakrabarti
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Jennifer Cooper
- Everglades Research and Education Center, Soil and Water Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - EunKyung Choi
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Carolina Ganan
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Bryn Tolchinsky
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA
| | - Eric W Triplett
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Samira H Daroub
- Everglades Research and Education Center, Soil and Water Sciences Department, University of Florida, Belle Glade, FL, 33430, USA
| | - Willm Martens-Habbena
- Fort Lauderdale Research and Education Center, Department of Microbiology and Cell Science, University of Florida, Davie, FL, 33314, USA.
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5
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Jiang C, Sun X, Liu Y, Zhu S, Wu K, Li H, Shui W. Karst tiankeng shapes the differential composition and structure of bacterial and fungal communities in karst land. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:32573-32584. [PMID: 36469271 DOI: 10.1007/s11356-022-24229-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
Abstract
Karst tiankeng are important biodiversity conservation reservoirs. However, the unique habitats of karst tiankeng affect microbial community structure remained poorly understood. In this study, we collected soil samples from karst tiankeng (TK) and karst land (KL) and subjected to high-throughput sequencing. Based on the classification of the total, abundance, and rare taxa for bacteria and fungi, a multivariate statistical analysis was carried out. The results revealed that bacterial community Shannon diversity and Pielou's evenness were highest in TK. The rare taxa were ubiquitous in all soil samples, while the higher Shannon diversity of the abundant taxa of TK may be related to the habitat preferences of species and niche differentiation. The community composition of bacterial and fungal sub-communities exhibited significant dissimilarity between TK and KL. The redundancy analysis further demonstrated that abundant taxa were environmentally more constrained than rare taxa. The bacterial and fungal networks of KL were more complex than TK. The keystones of the network transforms may suggest their significant role in the ecological function of the karst tiankeng ecosystem. This study represents the first reports of the characteristics of bacterial and fungal communities in karst tiankeng.
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Affiliation(s)
- Cong Jiang
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, People's Republic of China
| | - Xiang Sun
- College of Environment and Safety Engineering, Fujian Province, Fuzhou University, Fuzhou University Town, No. 2 Wulongjiang North Avenue, Fuzhou City, People's Republic of China
| | - Yuanmeng Liu
- College of Environment and Safety Engineering, Fujian Province, Fuzhou University, Fuzhou University Town, No. 2 Wulongjiang North Avenue, Fuzhou City, People's Republic of China
| | - Sufeng Zhu
- Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing, 100871, People's Republic of China
| | - Kexing Wu
- College of Environment and Safety Engineering, Fujian Province, Fuzhou University, Fuzhou University Town, No. 2 Wulongjiang North Avenue, Fuzhou City, People's Republic of China
| | - Hui Li
- College of Environment and Safety Engineering, Fujian Province, Fuzhou University, Fuzhou University Town, No. 2 Wulongjiang North Avenue, Fuzhou City, People's Republic of China
| | - Wei Shui
- College of Environment and Safety Engineering, Fujian Province, Fuzhou University, Fuzhou University Town, No. 2 Wulongjiang North Avenue, Fuzhou City, People's Republic of China.
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6
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Yin Y, Wang X, Hu Y, Li F, Cheng H. Soil bacterial community structure in the habitats with different levels of heavy metal pollution at an abandoned polymetallic mine. JOURNAL OF HAZARDOUS MATERIALS 2023; 442:130063. [PMID: 36182879 DOI: 10.1016/j.jhazmat.2022.130063] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Heavy metal pollution caused by mining activities can be harmful to soil microbiota, which are highly sensitive to heavy metal stress. This study aimed to investigate the response of soil bacterial communities to varying levels of heavy metal pollution in four types of habitats (i.e., tailing, remediation, natural recovery, and undisturbed areas) at an abandoned polymetallic mine by high-throughput 16 S rRNA gene sequencing, and to determine the dominant ecological processes and major factors driving the variations in bacterial community composition. The diversity and composition of bacterial communities varied significantly between soil habitats (p < 0.05). Heterogeneous selection played a crucial role in shaping the difference of bacterial community composition between distinct soil habitats. Redundancy analysis and Pearson correlation analysis revealed that the total contents of Cu and Zn were key factors causing the difference in bacterial community composition in the tailing and remediation areas, whereas bioavailable Mn and Cd, total nitrogen, available nitrogen, soil organic carbon, vegetation coverage, and plant diversity were key factors shaping the soil bacterial structure in the undisturbed and natural recovery areas. These findings provide insights into the distribution patterns of bacterial communities in soil habitats with different levels of heavy metal pollution, and the dominant ecological processes and the corresponding environmental drivers, and expand knowledge in bacterial assembly mechanisms in mining regions.
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Affiliation(s)
- Yue Yin
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Xiaojie Wang
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China; State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Yuanan Hu
- MOE Laboratory of Groundwater Circulation and Evolution, School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Fadong Li
- State Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
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7
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Malazarte J, Muotka T, Jyväsjärvi J, Lehosmaa K, Nyberg J, Huttunen KL. Bacterial communities in a subarctic stream network: Spatial and seasonal patterns of benthic biofilm and bacterioplankton. Mol Ecol 2022; 31:6649-6663. [PMID: 36198099 PMCID: PMC10091710 DOI: 10.1111/mec.16711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 09/01/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
Water-column bacterial communities are assembled by different mechanisms at different stream network positions, with headwater communities being controlled by mass effects (advection of bacteria from terrestrial soils) while downstream communities are mainly driven by environmental sorting. Conversely, benthic biofilms are colonized largely by the same set of taxa across the entire network. However, direct comparisons of biofilm and bacterioplankton communities along whole stream networks are rare. We used 16S rRNA gene amplicon sequencing to explore the spatiotemporal variability of benthic biofilm (2 weeks old vs. mature biofilm) and water-column communities at different network positions of a subarctic stream from early summer to late autumn. Amplicon sequence variant (ASV) richness of mature biofilm was about 2.5 times higher than that of early biofilm, yet the pattern of seasonality was the same, with the highest richness in midsummer. Biofilm bacterial richness was unrelated to network position whereas bacterioplankton diversity was negatively related to water residence time and distance from the source. This pattern of decreasing diversity along the network was strongest around midsummer and diminished greatly as water level increased towards autumn. Biofilm communities were phylogenetically clustered at all network positions while bacterioplankton assemblages were phylogenetically clustered only at the most downstream site. Both early and mature biofilm communities already differed significantly between upstream (1st order) and midstream (2nd order) sections. Network position was also related to variation in bacterioplankton communities, with upstream sites harbouring substantially more unique taxa (44% of all upstream taxa) than midstream (20%) or downstream (8%) sites. Some of the taxa that were dominant in downstream sections were already present in the upmost headwaters, and even in riparian soils, where they were very rare (relative abundance <0.01%). These patterns in species diversity and taxonomic and phylogenetic community composition of the riverine bacterial metacommunity were particularly strong for water-column communities, whereas both early and mature biofilm exhibited weaker spatial patterns. Our study demonstrated the benefits of studying bacterioplankton and biofilm communities simultaneously to allow testing of ecological hypotheses about biodiversity patterns in freshwater bacteria.
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Affiliation(s)
| | - Timo Muotka
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Jussi Jyväsjärvi
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Kaisa Lehosmaa
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
| | - Joel Nyberg
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
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8
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Zufiaurre A, Felip M, Camarero L, Sala-Faig M, Juhanson J, Bonilla-Rosso G, Hallin S, Catalan J. Bacterioplankton seasonality in deep high-mountain lakes. Front Microbiol 2022; 13:935378. [PMID: 36187988 PMCID: PMC9519062 DOI: 10.3389/fmicb.2022.935378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/08/2022] [Indexed: 12/04/2022] Open
Abstract
Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. High-mountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest decline, characterized by a dominance of Flavobacterium, and Limnohabitans. The rich core community and low random elements compared to other relatively small cold lakes can be attributed to its simple hydrological network in a poorly-vegetated catchment, the long water-residence time (ca. 4 years), and the long ice-cover duration; features common to many headwater deep high-mountain lakes.
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Affiliation(s)
- Aitziber Zufiaurre
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- Área de Biodiversidad, Gestión ambiental de Navarra-Nafarroako Ingurumenkudeaketa (GAN-NIK), Pamplona-Iruñea, Navarra, Spain
| | - Marisol Felip
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Lluís Camarero
- Centre d’Estudis Avançats de Blanes (CEAB), CSIC, Blanes, Catalonia, Spain
| | - Marc Sala-Faig
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Jaanis Juhanson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - German Bonilla-Rosso
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jordi Catalan
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- CSIC, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
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9
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The Resemblance between Bacterial Gut Colonization in Pigs and Humans. Microorganisms 2022; 10:microorganisms10091831. [PMID: 36144433 PMCID: PMC9500663 DOI: 10.3390/microorganisms10091831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/02/2022] [Accepted: 09/11/2022] [Indexed: 11/16/2022] Open
Abstract
Thorough understanding of the initial colonization process of human intestines is important to optimize the prevention of microbiota-associated diseases, and also to further improve the current microbial therapies. In recent years, therefore, colonization of the human gut has gained renewed interest. However, due to a lack of standardization of life events that might influence this early colonization process in humans, many generally accepted insights are based on deduction and assumption. In our review, we compare knowledge on colonization in humans with research in piglets, because the intestinal tract of pigs is remarkably similar to that of humans and the early-life events are more standardized. We assess potential similarities and challenge some concepts that have been widely accepted in human microbiota research. Bacterial colonization of the human gut is characterized by successive waves in a progressive process, to a complex gut microbiota community. After re-analyzing available data from piglets, we found that the bacterial colonization process is very similar in terms of the wave sequence and functionality of each wave. Moreover, based on the piglet data, we found that, in addition to external factors such as suckling and nutrition, the bacterial community itself appears to have a major influence on the colonization success of additional bacteria in the intestine. Thus, the colonization process in piglets might rely, at least in part, on niche dependency, an ecological principle to be considered in the intestinal colonization process in humans.
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10
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Wang X, Ren Y, Yu Z, Shen G, Cheng H, Tao S. Effects of environmental factors on the distribution of microbial communities across soils and lake sediments in the Hoh Xil Nature Reserve of the Qinghai-Tibetan Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 838:156148. [PMID: 35609688 DOI: 10.1016/j.scitotenv.2022.156148] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/07/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Comparison of microbial community diversity and composition of terrestrial and aquatic ecosystems in undisturbed regions could expand our understanding on the mechanisms of microbial community assembly and ecosystem responses to environmental change. This study investigated the spatial distribution of bacterial community diversity and composition in the lakeshore soils and lake sediments from one of the best preserved nature reserves, Hoh Xil on the Qinghai-Tibetan Plateau, and explored the corresponding environmental drivers. A total of 36 sediment and soil samples were collected from six alpine lakes and the corresponding shore zones, and their bacterial community structure was identified by high-throughput 16S rRNA gene sequencing. Significant difference (p < 0.05) in diversity and composition of bacterial communities between the soils and sediments was observed. Heterogeneous selection played a dominant role in shaping the spatial variations of bacterial communities between the soils and sediments. Results of canonical correspondence analysis showed that the difference in composition of bacterial communities at OTU level between the soils and sediments was mainly determined by the mean annual temperature, salinity, and contents of total organic carbon and total nitrogen. Structural equation modeling revealed that salinity played a significantly direct role in soil bacterial composition, while mean annual temperature indirectly affected the bacterial composition mainly through changing soil salinity. In contrast, the sediment bacterial composition was directly influenced primarily by the contents of total organic carbon and total nitrogen, while pH also had an important indirect effect on sediment bacterial composition. These results shed light on the distribution patterns of bacterial communities between lakeshore soils and lake sediments in high-altitude permafrost regions, and the major ecological processes and environmental drivers that shaped their bacterial communities, and provide insight into the mechanisms underlying microbial community assembly in such regions.
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Affiliation(s)
- Xiaojie Wang
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China; University of Chinese Academy of Sciences, Beijing 100049, China; MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Yuxuan Ren
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Zhiqiang Yu
- State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Guofeng Shen
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
| | - Hefa Cheng
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China.
| | - Shu Tao
- MOE Laboratory for Earth Surface Processes, College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
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11
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Qi Q, Hu C, Lin J, Wang X, Tang C, Dai Z, Xu J. Contamination with multiple heavy metals decreases microbial diversity and favors generalists as the keystones in microbial occurrence networks. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119406. [PMID: 35561794 DOI: 10.1016/j.envpol.2022.119406] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/01/2022] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
Soil contamination with multiple heavy metals poses threats to human health and ecosystem functioning. Using the Nemerow pollution index, which considers the effects of multiple heavy metals, we compared the diversity and composition of bacteria, fungi and protists and their potential interactions in response to a multi-metal contamination gradient. Multi-metal contamination significantly altered the community composition of bacteria, fungi and protists, and the degree of alteration increased with increasing severity of contamination. The alpha-diversity of bacteria, fungi and protists significantly decreased with increasing contamination level. The dominant generalists, found in all soil samples, were Gammaproteobacteria, Chloroflexi and Bacillus sp, whereas the dominant specialists were Anaerolineaceae, Entoloma sp. and Sandonidae_X sp. The relative abundances of generalists were positively correlated, whereas those of specialists were negatively correlated, with the Nemerow pollution index. In addition, the complexity of the microbial co-occurrence network increased with increasing contamination level. Generalists, rather than specialists, were the keystones in the microbial co-occurrence network and played a crucial role in adaptation to multi-metal contamination through enhanced potential interactions within the entire microbiome. Our results provide insights into the ecological effects of multi-metal contamination on the soil microbiome and will help to develop bio-remediation technologies for contaminated soils.
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Affiliation(s)
- Qian Qi
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Caixia Hu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Jiahui Lin
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Xuehua Wang
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China
| | - Caixian Tang
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Zhongmin Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China; The Rural Development Academy at Zhejiang University, Zhejiang University, Hangzhou, 310058, China.
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058, China; Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Zhejiang University, Hangzhou, 310058, China; The Rural Development Academy at Zhejiang University, Zhejiang University, Hangzhou, 310058, China
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12
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Abdullah Al M, Xue Y, Xiao P, Xu J, Chen H, Mo Y, Shimeta J, Yang J. Community assembly of microbial habitat generalists and specialists in urban aquatic ecosystems explained more by habitat type than pollution gradient. WATER RESEARCH 2022; 220:118693. [PMID: 35667165 DOI: 10.1016/j.watres.2022.118693] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/19/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Urban freshwater ecosystems have important ecosystem functions, provide habitats for diverse microbial communities and are susceptible to multiple interconnected factors such as environmental pollution. Despite the ecological significance of bacteria and microeukaryotes, little is known about how their community assembly responds to various environmental factors across water and sediment habitats and ecological processes shaping them. Here, environmental DNA-based approaches were used to investigate the community assembly processes of bacteria and microeukaryotes (including habitat generalists and specialists) in urban water and sediment across an urban-pollution gradient in Wuhan, central China. The diversity, community composition and potential function of bacteria and microeukaryotes showed significantly stronger variation between water and sediment than across an urban pollution gradient. Although, bacterial and microeukaryotic community assemblies were dominated by strong selection processes in both water and sediment habitats, but a contrasting community assembly mechanism was identified between habitat generalists and specialists. Bacterial and microeukaryotic communities showed a greater response to physicochemical variability in water, while a strong distance-decay relationship was found in sediment. Further, cross-kingdom microbial network analysis revealed strong modular associations of bacteria and microeukaryotes, meanwhile, microeukaryotic habitat specialists might be keystone, but generalists have higher proportion of connections in the networks. This study provides significant insights into the response of bacteria and microeukaryotes to different urban pollutions between water and sediment, and the ecological processes structuring microbial community dynamics across habitat types under anthropogenic disturbances.
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Affiliation(s)
- Mamun Abdullah Al
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Xue
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Peng Xiao
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Jing Xu
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, China
| | - Huihuang Chen
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Mo
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jeff Shimeta
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Jun Yang
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
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13
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Ferrer A, Heath KD, Mosquera SL, Suaréz Y, Dalling JW. Assembly of wood-inhabiting archaeal, bacterial and fungal communities along a salinity gradient: common taxa are broadly distributed but locally abundant in preferred habitats. FEMS Microbiol Ecol 2022; 98:6566339. [PMID: 35404430 DOI: 10.1093/femsec/fiac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/12/2022] Open
Abstract
Wood decomposition in water is a key ecosystem process driven by diverse microbial taxa that likely differ in their affinities for freshwater, estuarine, and marine habitats. How these decomposer communities assemble in situ or potentially colonize from other habitats remains poorly understood. At three watersheds on Coiba Island, Panama, we placed replicate sections of branch wood of a single tree species on land, and in freshwater, estuarine and marine habitats that constitute a downstream salinity gradient. We sequenced archaea, bacteria and fungi from wood samples collected after 3, 9, and 15 months to examine microbial community composition, and to examine habitat specificity and abundance patterns. We found these microbial communities were broadly structured by similar factors, with a strong effect of salinity, but little effect of watershed identity on compositional variation. Moreover, common aquatic taxa were also present in wood incubated on land. Our results suggest that taxa either dispersed to both terrestrial and aquatic habitats, or that microbes with broad habitat ranges were initially present in the wood as endophytes. Nonetheless, these habitat generalists varied greatly in abundance across habitats suggesting an important role for habitat filtering in maintaining distinct aquatic communities in freshwater, estuarine and marine habitats.
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Affiliation(s)
- Astrid Ferrer
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Sergio L Mosquera
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - Yaraví Suaréz
- Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
| | - James W Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.,Smithsonian Tropical Research Institute, Apartado 0843-03092, Balboa, Ancon, Republic of Panama
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14
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Geng M, Zhang W, Hu T, Wang R, Cheng X, Wang J. Eutrophication causes microbial community homogenization via modulating generalist species. WATER RESEARCH 2022; 210:118003. [PMID: 34982976 DOI: 10.1016/j.watres.2021.118003] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/14/2021] [Accepted: 12/21/2021] [Indexed: 05/27/2023]
Abstract
Eutrophication substantially influences the community structure of aquatic organisms and has become a major threat to biodiversity. However, whether eutrophication is linked to homogenization of microbial communities and the possible underlying mechanisms are poorly understood. Here, we studied bacterial and fungal communities from water and sediments of 40 shallow lakes in the Yangtze-Huaihe River basin, a representative area characterized by intensifying eutrophication in China, and further examined the beta diversity patterns and underlying mechanisms under eutrophication conditions. Our results indicate that eutrophication generally caused biotic homogenization of bacterial and fungal communities in both habitats showing decreased community variations for the sites with a higher trophic state index (TSI). In the two habitats, community dissimilarities were positively correlated with TSI changes for both taxonomic groups, while the local contribution to beta diversity (LCBD) remarkably declined with increasing TSI for the fungal community. These phenomena were consistent with the pivotal importance of the TSI in statistically accounting for beta diversity of bacterial and fungal communities in both habitats. In addition, we found that physicochemical factors such as water temperature and pH were also important for bacterial and fungal communities in water, while heavy metal elements were important for the communities in sediments. Interestingly, generalist species, rather than specialist species, were revealed to more dominantly affect the variations in beta diversity along the trophic gradient, which were quantified by Bray-Curtis dissimilarity and LCBD. Collectively, our findings reveal the importance of generalist species in contributing to the change of beta diversity of microbial communities along trophic gradients, which have profound implications for a comprehensive understanding of the effects of eutrophication on microbial community.
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Affiliation(s)
- Mengdie Geng
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Nanjing 210008, China
| | - Weizhen Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Nanjing 210008, China; Center for the Pan-third Pole Environment, Lanzhou University, Lanzhou 730000, China
| | - Ting Hu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Nanjing 210008, China
| | - Rong Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Nanjing 210008, China
| | - Xiaoying Cheng
- School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China.
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Nanjing 210008, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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15
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Shraim R, Nieuwenhuis BPS. The search for Schizosaccharomyces fission yeasts in environmental meta-transcriptomes. Yeast 2021; 39:83-94. [PMID: 34967063 DOI: 10.1002/yea.3689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/09/2021] [Accepted: 12/23/2021] [Indexed: 11/07/2022] Open
Abstract
Fission yeast is an important model organism in evolutionary genetics and cell biology research. Nevertheless, most research is limited to a single laboratory strain and knowledge of its natural occurrence is limited, which reduces our understanding of its life history and hinders isolation of new strains from nature. Understanding the natural diversity of fission yeast can provide insight into its genetic and phenotypic diversity and the evolutionary processes that shaped these. Here we aimed to identify candidate natural habitats of fission yeasts by searching through a large collection of publicly available environmental metatranscriptomic datasets. Using a custom pipeline, we processed over 13,000 NCBI SRA accessions, from a wide range of 34 different environmental categories. Overall, we found a very low abundance of putative yeast transcripts, with most fission yeast signatures coming from the categories of 'food' and 'terrestrial arthropods'. Additionally, a signal could be found in a variety of marine and fresh aquatic habitats. Our results do not provide a conclusive answer on the natural habitat of fission yeasts, but our analysis further narrows the range of locations where fission yeasts naturally occur.
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Affiliation(s)
- Rasha Shraim
- The SFI Centre for Research Training in Genomics Data Sciences, National University of Ireland Galway and Department of Public Health and Primary Care, School of Medicine, Trinity College Dublin, Republic of Ireland.,Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Germany
| | - Bart P S Nieuwenhuis
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Germany
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16
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Dal Bello M, Lee H, Goyal A, Gore J. Resource-diversity relationships in bacterial communities reflect the network structure of microbial metabolism. Nat Ecol Evol 2021; 5:1424-1434. [PMID: 34413507 DOI: 10.1038/s41559-021-01535-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 07/14/2021] [Indexed: 02/06/2023]
Abstract
The relationship between the number of available nutrients and community diversity is a central question in ecological research that remains unanswered. Here we studied the assembly of hundreds of soil-derived microbial communities on a wide range of well-defined resource environments, from single carbon sources to combinations of up to 16. We found that, while single resources supported multispecies communities varying from 8 to 40 taxa, mean community richness increased only one-by-one with additional resources. Cross-feeding could reconcile these seemingly contrasting observations, with the metabolic network seeded by the supplied resources explaining the changes in richness due to both the identity and the number of resources, as well as the distribution of taxa across different communities. By using a consumer-resource model incorporating the inferred cross-feeding network, we provide further theoretical support to our observations and a framework to link the type and number of environmental resources to microbial community diversity.
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Affiliation(s)
- Martina Dal Bello
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Hyunseok Lee
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Akshit Goyal
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jeff Gore
- Physics of Living Systems Group, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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17
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Caillon F, Besemer K, Peduzzi P, Schelker J. Soil microbial inoculation during flood events shapes headwater stream microbial communities and diversity. MICROBIAL ECOLOGY 2021; 82:591-601. [PMID: 33532913 PMCID: PMC8463373 DOI: 10.1007/s00248-021-01700-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/21/2021] [Indexed: 05/10/2023]
Abstract
Flood events are now recognized as potentially important occasions for the transfer of soil microbes to stream ecosystems. Yet, little is known about these "dynamic pulses of microbial life" for stream bacterial community composition (BCC) and diversity. In this study, we explored the potential alteration of stream BCC by soil inoculation during high flow events in six pre-alpine first order streams and the larger Oberer Seebach. During 1 year, we compared variations of BCC in soil water, stream water and in benthic biofilms at different flow conditions (low to intermediate flows versus high flow). Bacterial diversity was lowest in biofilms, followed by soils and highest in headwater streams and the Oberer Seebach. In headwater streams, bacterial diversity was significantly higher during high flow, as compared to low flow (Shannon diversity: 7.6 versus 7.9 at low versus high flow, respectively, p < 0.001). Approximately 70% of the bacterial operational taxonomic units (OTUs) from streams and stream biofilms were the same as in soil water, while in the latter one third of the OTUs were specific to high flow conditions. These soil high-flow OTUs were also found in streams and biofilms at other times of the year. These results demonstrate the relevance of floods in generating short and reoccurring inoculation events for flowing waters. Moreover, they show that soil microbial inoculation during high flow enhances microbial diversity and shapes fluvial BCC even during low flow. Hence, soil microbial inoculation during floods could act as a previously overlooked driver of microbial diversity in headwater streams.
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Affiliation(s)
- Florian Caillon
- WasserCluster Lunz/Biological Station GmbH, A-3293, Lunz am See, Austria.
- Division of Limnology, Department of Functional and Evolutionary Ecology, University of Vienna, A-1090, Vienna, Austria.
| | - Katharina Besemer
- Division of Limnology, Department of Functional and Evolutionary Ecology, University of Vienna, A-1090, Vienna, Austria
| | - Peter Peduzzi
- Division of Limnology, Department of Functional and Evolutionary Ecology, University of Vienna, A-1090, Vienna, Austria
| | - Jakob Schelker
- WasserCluster Lunz/Biological Station GmbH, A-3293, Lunz am See, Austria
- Division of Limnology, Department of Functional and Evolutionary Ecology, University of Vienna, A-1090, Vienna, Austria
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18
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Four species of bacteria deterministically assemble to form a stable biofilm in a millifluidic channel. NPJ Biofilms Microbiomes 2021; 7:64. [PMID: 34354076 PMCID: PMC8342524 DOI: 10.1038/s41522-021-00233-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023] Open
Abstract
Multispecies microbial adherent communities are widespread in nature and organisms, although the principles of their assembly and development remain unclear. Here, we test the possibility of establishing a simplified but relevant model of multispecies biofilm in a non-invasive laboratory setup for the real-time monitoring of community development. We demonstrate that the four chosen species (Bacillus thuringiensis, Pseudomonas fluorescens, Kocuria varians, and Rhodocyclus sp.) form a dynamic community that deterministically reaches its equilibrium after ~30 h of growth. We reveal the emergence of complexity in this simplified community as reported by an increase in spatial heterogeneity and non-monotonic developmental kinetics. Importantly, we find interspecies interactions consisting of competition for resources-particularly oxygen-and both direct and indirect physical interactions. The simplified experimental model opens new avenues to the study of adherent bacterial communities and their behavior in the context of rapid global change.
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19
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Hugoni M, Nunan N, Thioulouse J, Dubost A, Abrouk D, Martins JMF, Goffner D, Prigent-Combaret C, Grundmann G. Small-Scale Variability in Bacterial Community Structure in Different Soil Types. MICROBIAL ECOLOGY 2021; 82:470-483. [PMID: 33443587 DOI: 10.1007/s00248-020-01660-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Microbial spatial distribution has mostly been studied at field to global scales (i.e., ecosystem scales). However, the spatial organization at small scales (i.e., centimeter to millimeter scales), which can help improve our understanding of the impacts of spatial communities structure on microbial functioning, has received comparatively little attention. Previous work has shown that small-scale spatial structure exists in soil microbial communities, but these studies have not compared soils from geographically distant locations, nor have they utilized community ecology approaches, such as the core and satellite hypothesis and/or abundance-occupancy relationships, often used in macro-ecology, to improve the description of the spatial organization of communities. In the present work, we focused on bacterial diversity (i.e., 16S rRNA gene sequencing) occurring in micro-samples from a variety of locations with different pedo-climatic histories (i.e., from semi-arid, alpine, and temperate climates) and physicochemical properties. The forms of ecological spatial relationships in bacterial communities (i.e., occupancy-frequency and abundance-occupancy) and taxa distributions (i.e., habitat generalists and specialists) were investigated. The results showed that bacterial composition differed in the four soils at the small scale. Moreover, one soil presented a satellite mode distribution, whereas the three others presented bimodal distributions. Interestingly, numerous core taxa were present in the four soils among which 8 OTUs were common to the four sites. These results confirm that analyses of the small-scale spatial distribution are necessary to understand consequent functional processes taking place in soils, affecting thus ecosystem functioning.
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Affiliation(s)
- Mylène Hugoni
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France.
| | - Naoise Nunan
- Institute of Ecology and Environmental Sciences - Paris, CNRS - Sorbonne Université, 4 place Jussieu, 75005, Paris, France
- Department of Soil and Environment, Swedish University of Agricultural Sciences, 75007, Uppsala, Sweden
| | - Jean Thioulouse
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, F-69622 Villeurbanne, France
| | - Audrey Dubost
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
| | - Danis Abrouk
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
| | - Jean M F Martins
- Université Grenoble Alpes, CNRS, IRD, IGE UMR 5001, 38000, Grenoble, France
| | - Deborah Goffner
- Unité Mixte Internationale CNRS 3189 « Environment, Health and Societies », Faculté de Médecine, 51 Bd Pierre Dramard, 13344, Marseille, France
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
| | - Geneviève Grundmann
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR Ecologie Microbienne, INRA, UMR1418, 69220, F-69622, Villeurbanne Cedex, France
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20
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Liu J, Su J, Zhang M, Luo Z, Li X, Chai B. Bacterial Community Spacing Is Mainly Shaped by Unique Species in the Subalpine Natural Lakes of China. Front Microbiol 2021; 12:669131. [PMID: 34276600 PMCID: PMC8282455 DOI: 10.3389/fmicb.2021.669131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/28/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial communities have been described as early indicators of both regional and global climatic change and play a critical role in the global biogeochemical cycle. Exploring the mechanisms that determine the diversity patterns of bacterial communities and how they share different habitats along environmental gradients are, therefore, a central theme in microbial ecology research. We characterized the diversity patterns of bacterial communities in Pipahai Lake (PPH), Mayinghai Lake (MYH), and Gonghai Lake (GH), three subalpine natural lakes in Ningwu County, Shanxi, China, and analyzed the distribution of their shared and unique taxa (indicator species). Results showed that the species composition and structure of bacterial communities were significantly different among the three lakes. Both the structure of the entire bacterial community and the unique taxa were significantly influenced by the carbon content (TOC and IC) and space distance; however, the structure of the shared taxa was affected by conductivity (EC), pH, and salinity. The structure of the entire bacterial community and unique taxa were mainly affected by the same factors, suggesting that unique taxa may be important in maintaining the spatial distribution diversity of bacterial communities in subalpine natural freshwater lakes. Our results provide new insights into the diversity maintenance patterns of the bacterial communities in subalpine lakes, and suggest dispersal limitation on bacterial communities between adjacent lakes, even in a small local area. We revealed the importance of unique taxa in maintaining bacterial community structure, and our results are important in understanding how bacterial communities in subalpine lakes respond to environmental change in local habitats.
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Affiliation(s)
- Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
| | - Jiahe Su
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
| | - Meiting Zhang
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
| | - Zhengming Luo
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China.,Department of Geography, Xinzhou Teachers University, Xinzhou, China
| | - Xiaoqi Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Shanxi Key Laboratory of Ecological Restoration on the Loess Plateau, Shanxi University, Taiyuan, China.,Field Scientific Observation and Research Station of the Ministry of Education of Shanxi Subalpine Grassland Ecosystem, Shanxi University, Taiyuan, China
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21
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Comprehensive Scanning of Prophages in Lactobacillus: Distribution, Diversity, Antibiotic Resistance Genes, and Linkages with CRISPR-Cas Systems. mSystems 2021; 6:e0121120. [PMID: 34060909 PMCID: PMC8269257 DOI: 10.1128/msystems.01211-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Prophage integration, release, and dissemination exert various effects on host bacteria. In the genus Lactobacillus, they may cause bacteriophage contamination during fermentation and even regulate bacterial populations in the gut. However, little is known about their distribution, genetic architecture, and relationships with their hosts. Here, we conducted prophage prediction analysis on 1,472 genomes from 16 different Lactobacillus species and found prophage fragments in almost all lactobacilli (99.8%), with 1,459 predicted intact prophages identified in 64.1% of the strains. We present an uneven prophage distribution among Lactobacillus species; multihabitat species retained more prophages in their genomes than restricted-habitat species. Characterization of the genome features, average nucleotide identity, and landscape visualization presented a high genome diversity of Lactobacillus prophages. We detected antibiotic resistance genes in more than 10% of Lactobacillus prophages and validated that the occurrence of resistance genes conferred by prophage integration was possibly associated with phenotypic resistance in Lactobacillus plantarum. Furthermore, our broad and comprehensive examination of the distribution of CRISPR-Cas systems across the genomes predicted type I and type III systems as potential antagonistic elements of Lactobacillus prophage. IMPORTANCE Lactobacilli are inherent microorganisms in the human gut and are widely used in the food processing industries due to their probiotic properties. Prophages were reportedly hidden in numerous Lactobacillus genomes and can potentially contaminate entire batches of fermentation or modulate the intestinal microecology once they are released. Therefore, a comprehensive scanning of prophages in Lactobacillus is essential for the safety evaluation and application development of probiotic candidates. We show that prophages are widely distributed among lactobacilli; however, intact prophages are more common in multihabitat species and display wide variations in genome feature, integration site, and genomic organization. Our data of the prophage-mediated antibiotic resistance genes (ARGs) and the resistance phenotype of lactobacilli provide evidence for deciphering the putative role of prophages as vectors of the ARGs. Furthermore, understanding the association between prophages and CRISPR-Cas systems is crucial to appreciate the coevolution of phages and Lactobacillus.
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22
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Sonthiphand P, Kraidech S, Polart S, Chotpantarat S, Kusonmano K, Uthaipaisanwong P, Rangsiwutisak C, Luepromchai E. Arsenic speciation, the abundance of arsenite-oxidizing bacteria and microbial community structures in groundwater, surface water, and soil from a gold mine. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART A, TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING 2021; 56:769-785. [PMID: 34038319 DOI: 10.1080/10934529.2021.1927421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 04/26/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
The arsenic speciation, the abundance of arsenite-oxidizing bacteria, and microbial community structures in the groundwater, surface water, and soil from a gold mining area were explored using the PHREEQC model, cloning-ddPCR of the aioA gene, and high-throughput sequencing of the 16S rRNA gene, respectively. The analysis of the aioA gene showed that arsenite-oxidizing bacteria retrieved from groundwater, surface water, and soil were associated with Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. In groundwaters from the mining area, there were relatively high ratios of aioA/total 16S rRNA gene copies and the dominance of As5+, which suggested the presence and activity of arsenite-oxidizing bacteria. Metagenomic analysis revealed that the majority of the soil and surface water microbiomes were Proteobacteria, Actinobacteria, Bacteroidetes, and Chloroflexi, whereas the groundwater microbiomes were dominated exclusively by Betaproteobacteria and Alphaproteobacteria. Geochemical factors influencing the microbial structure in the groundwater were As, residence time, and groundwater flowrate, while those showing a positive correlation to the microbial structure in the surface water were TOC, ORP, and DO. This study provides insights into the groundwater, surface water, and soil microbiomes from a gold mine and expands the current understanding of the diversity and abundance of arsenite-oxidizing bacteria, playing a vital role in global As cycling.
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Affiliation(s)
- Prinpida Sonthiphand
- Faculty of Science, Department of Biology, Mahidol University, Bangkok, Ratchathewi, Thailand
| | - Supeerapat Kraidech
- International Postgraduate Program in Hazardous Substance and Environmental Management, Chulalongkorn University, Bangkok, Thailand
| | - Saowarod Polart
- Faculty of Science, Department of Biology, Mahidol University, Bangkok, Ratchathewi, Thailand
| | - Srilert Chotpantarat
- Faculty of Science, Department of Geology, Chulalongkorn University, Thailand
- Research Program on Controls of Hazardous Contaminants in Raw Water Resources for Water Scarcity Resilience, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Thailand
- Research Unit of Site Remediation on Metals Management from Industry and Mining (Site Rem), Chulalongkorn University, Bangkok, Thailand
| | - Kanthida Kusonmano
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
- Systems Biology and Bioinformatics Research Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Pichahpuk Uthaipaisanwong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Chalida Rangsiwutisak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Ekawan Luepromchai
- Research Program on Remediation Technologies for Petroleum Contamination, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, Thailand
- Microbial Technology for Marine Pollution Treatment Research Unit, Department of Microbiology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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23
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Sonthiphand P, Rattanaroongrot P, Mek-Yong K, Kusonmano K, Rangsiwutisak C, Uthaipaisanwong P, Chotpantarat S, Termsaithong T. Microbial community structure in aquifers associated with arsenic: analysis of 16S rRNA and arsenite oxidase genes. PeerJ 2021; 9:e10653. [PMID: 33510973 PMCID: PMC7798605 DOI: 10.7717/peerj.10653] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/04/2020] [Indexed: 11/20/2022] Open
Abstract
The microbiomes of deep and shallow aquifers located in an agricultural area, impacted by an old tin mine, were explored to understand spatial variation in microbial community structures and identify environmental factors influencing microbial distribution patterns through the analysis of 16S rRNA and aioA genes. Although Proteobacteria, Cyanobacteria, Actinobacteria, Patescibacteria, Bacteroidetes, and Epsilonbacteraeota were widespread across the analyzed aquifers, the dominant taxa found in each aquifer were unique. The co-dominance of Burkholderiaceae and Gallionellaceae potentially controlled arsenic immobilization in the aquifers. Analysis of the aioA gene suggested that arsenite-oxidizing bacteria phylogenetically associated with Alpha-, Beta-, and Gamma proteobacteria were present at low abundance (0.85 to 37.13%) and were more prevalent in shallow aquifers and surface water. The concentrations of dissolved oxygen and total phosphorus significantly governed the microbiomes analyzed in this study, while the combination of NO3 --N concentration and oxidation-reduction potential significantly influenced the diversity and abundance of arsenite-oxidizing bacteria in the aquifers. The knowledge of microbial community structures and functions in relation to deep and shallow aquifers is required for further development of sustainable aquifer management.
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Affiliation(s)
- Prinpida Sonthiphand
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Kasarnchon Mek-Yong
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Kanthida Kusonmano
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Systems Biology and Bioinformatics Research Laboratory, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Chalida Rangsiwutisak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Pichahpuk Uthaipaisanwong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Srilert Chotpantarat
- Department of Geology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Research Program on Controls of Hazardous Contaminants in Raw Water Resources for Water Scarcity Resilience, Center of Excellence on Hazardous Substance Management (HSM), Chulalongkorn University, Bangkok, Thailand.,Research Unit of Green Mining (GMM), Chulalongkorn University, Bangkok, Thailand
| | - Teerasit Termsaithong
- Learning Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.,Theoretical and Computational Science Center (TaCS), King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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24
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Serbent MP, Dos Anjos Borges LG, Quadros A, Marconatto L, Tavares LBB, Giongo A. Prokaryotic and microeukaryotic communities in an experimental rice plantation under long-term use of pesticides. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:2328-2341. [PMID: 32880839 DOI: 10.1007/s11356-020-10614-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/23/2020] [Indexed: 06/11/2023]
Abstract
Conventional agricultural practices, such as rice plantations, often contaminate the soil and water with xenobiotics. Here we evaluated the microbiota composition in experimental rice planting with a record of prolonged pesticide use, using 16S and 18S rRNA amplicon sequencing. We investigated four components of a complete agricultural system: affluent water (A), rice rhizosphere soil (R), sediment from a storage pond (S), and effluent (E) water (drained from the storage pond). Despite the short spatial distance between our sites, the beta diversity analysis of bacterial communities showed two well-defined clusters, separating the water and sediment/rhizosphere samples; rhizosphere and sediment were richer while the effluent was less diverse. Overall, the site with the highest evenness was the rhizosphere. Unlike the bacterial communities, Shannon diversity of microeukaryotes was significantly different between A and E. The effluent presented the lowest values for all ecological indexes tested and differed significantly from all sampled sites, except on evenness. When mapped the metabolic pathways, genes corresponding to the degradation of aromatic compounds, including genes related to pesticide degradation, were identified. The most abundant genes were related to the degradation of benzoate. Our results indicate that the effluent is a selective environment for fungi. Interestingly, the overall fungal diversity was higher in the affluent, the water that reached the system before pesticide application, and where the prokaryotic diversity was the lowest. The affluent and effluent seem to have the lowest environmental quality, given the presence of bacteria genera previously recorded in environments with high concentrations of pesticide residues. The microbiota, environmental characteristics, and pesticide residues should be further studied and try to elucidate the potential for pesticide degradation by natural consortia. Thus, extensive comparative studies are needed to clarify the microbial composition, diversity, and functioning of rice cultivation environments, and how pesticide use changes may reflect differences in microbial structure.
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Affiliation(s)
- Maria Pilar Serbent
- Santa Catarina State University - UDESC, Ibirama, Brazil.
- Environmental Engineering Graduate Program, PPGEA, Regional University of Blumenau - FURB, Blumenau, Brazil.
| | - Luiz Gustavo Dos Anjos Borges
- Institute of Petroleum and Natural Resources (IPR), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Aline Quadros
- Pumpkin Science Communication, Porto Alegre, RS, Brazil
| | - Letícia Marconatto
- Institute of Petroleum and Natural Resources (IPR), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | | | - Adriana Giongo
- Environmental Engineering Graduate Program, PPGEA, Regional University of Blumenau - FURB, Blumenau, Brazil
- Institute of Petroleum and Natural Resources (IPR), Pontifical Catholic University of Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
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25
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Babalola OO, Fadiji AE, Enagbonma BJ, Alori ET, Ayilara MS, Ayangbenro AS. The Nexus Between Plant and Plant Microbiome: Revelation of the Networking Strategies. Front Microbiol 2020; 11:548037. [PMID: 33013781 PMCID: PMC7499240 DOI: 10.3389/fmicb.2020.548037] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022] Open
Abstract
The diversity of plant-associated microbes is enormous and complex. These microbiomes are structured and form complex interconnected microbial networks that are important in plant health and ecosystem functioning. Understanding the composition of the microbiome and their core function is important in unraveling their networking strategies and their potential influence on plant performance. The network is altered by the host plant species, which in turn influence the microbial interaction dynamics and co-evolution. We discuss the plant microbiome and the complex interplay among microbes and between their host plants. We provide an overview of how plant performance is influenced by the microbiome diversity and function.
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Affiliation(s)
- Olubukola Oluranti Babalola
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Ayomide E Fadiji
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Ben J Enagbonma
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Elizabeth T Alori
- Department of Crop and Soil Sciences, Landmark University, Omu-Aran, Nigeria
| | - Modupe S Ayilara
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Ayansina S Ayangbenro
- Food Security and Safety Niche, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
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26
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Ferrer A, Heath KD, Canam T, Flores HD, Dalling JW. Contribution of fungal and invertebrate communities to wood decay in tropical terrestrial and aquatic habitats. Ecology 2020; 101:e03097. [PMID: 32415862 DOI: 10.1002/ecy.3097] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 02/26/2020] [Accepted: 04/01/2020] [Indexed: 11/06/2022]
Abstract
Wood is a major carbon input into aquatic ecosystems and is thought to decay slowly, yet surprisingly little terrestrial carbon accumulates in marine sediments. A better mechanistic understanding of how habitat conditions and decomposer communities influence wood decay processes along the river-estuary-ocean continuum can address this seeming paradox. We measured mass loss, wood element, and polymer concentrations, quantified invertebrate-induced decay, and sequenced fungal communities associated with replicate sections of Guazuma branch wood submerged in freshwater, estuarine, and near-shore marine habitats and placed on the soil surface in nearby terrestrial habitats in three watersheds in the tropical eastern Pacific. Over 15 months, we found that wood decayed at similar rates in estuarine, marine, and terrestrial sites, reflecting the combined activity of invertebrate and microbial decomposers. In contrast, in the absence of shipworms (Teredinidae), which accounted for ~40% of wood mass loss in the estuarine habitats, decay proceeded more slowly in freshwater. Over the experiment, wood element chemistry diverged among freshwater, estuarine, and marine habitats, due to differences in both nutrient losses (e.g., potassium and phosphorus) and gains (e.g., calcium and aluminum) through decay. Similarly, we observed changes in wood polymer content, with the highest losses of cellulose, hemicellulose, and lignin moieties in the marine habitat. Aquatic fungal communities were strongly dominated by ascomycetes (88-99% of taxa), compared to terrestrial communities (55% ascomycetes). Large differences in fungal diversity were also observed across habitats with threefold higher richness in terrestrial than freshwater habitats and twofold higher diversity in freshwater than estuarine/marine habitats. Divergent decay trajectories across habitats were associated with widespread order-level differences in fungal composition, with distinct communities found in freshwater, estuarine and marine habitats. However, few individual taxa that were significantly associated with mass loss were broadly distributed, suggesting a high level of functional redundancy. The rapid processing of wood entering tropical rivers by microbes and invertebrates, comparable to that on land, indicates that estuaries and coastal oceans are hotspots not just for the processing of particulate and dissolved organic carbon, but also for woody debris and for the breakdown of lignin, the most recalcitrant polymer in plant tissue.
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Affiliation(s)
- Astrid Ferrer
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Katy D Heath
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Thomas Canam
- Department of Biological Sciences, Eastern Illinois University, Charleston, Illinois, 61920, USA
| | - Hector D Flores
- Department of Biological Sciences, Eastern Illinois University, Charleston, Illinois, 61920, USA
| | - James W Dalling
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, USA.,Smithsonian Tropical Research Institute, Apartado, Balboa, Ancon, 0843-03092, Republic of Panama
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27
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Pedrinho A, Mendes LW, Merloti LF, Andreote FD, Tsai SM. The natural recovery of soil microbial community and nitrogen functions after pasture abandonment in the Amazon region. FEMS Microbiol Ecol 2020; 96:5876346. [DOI: 10.1093/femsec/fiaa149] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/23/2020] [Indexed: 12/18/2022] Open
Abstract
ABSTRACT
We assessed the impacts of forest-to-pasture conversion on the dynamic of soil microbial communities, especially those involved in the N-cycle, and their potential functions, using DNA-metagenomic sequencing coupled with the quantification of marker genes for N-cycling. We also evaluated whether the community's dynamic was reestablished with secondary forest growth. In general, the microbial community structure was influenced by changes in soil chemical properties. Aluminum and nitrate significantly correlated to community structure and with 12 out of 21 microbial phyla. The N-related microbial groups and their potential functions were also affected by land-use change, with pasture being clearly different from primary and secondary forest systems. The microbial community analysis demonstrated that forest-to-pasture conversion increased the abundance of different microbial groups related to nitrogen fixation, including Bacteroidetes, Chloroflexi and Firmicutes. In contrast, after pasture abandonment and with the secondary forest regeneration, there was an increase in the abundance of Proteobacteria taxa and denitrification genes. Our multi-analytical approach indicated that the secondary forest presented some signs of resilience, suggesting that the N-related microbial groups and their potential functions can be recovered over time with implications for future ecological restoration programs.
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Affiliation(s)
- Alexandre Pedrinho
- Soil Microbiology Laboratory, Luiz de Queiroz College of Agriculture (ESALQ), University of Sao Paulo, Avenida Padua Dias 11, Piracicaba, Sao Paulo 13418-900, Brazil
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo, Avenida Centenario 303, Piracicaba, Sao Paulo 13416-000, Brazil
| | - Lucas William Mendes
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo, Avenida Centenario 303, Piracicaba, Sao Paulo 13416-000, Brazil
| | - Luis Fernando Merloti
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo, Avenida Centenario 303, Piracicaba, Sao Paulo 13416-000, Brazil
| | - Fernando Dini Andreote
- Soil Microbiology Laboratory, Luiz de Queiroz College of Agriculture (ESALQ), University of Sao Paulo, Avenida Padua Dias 11, Piracicaba, Sao Paulo 13418-900, Brazil
| | - Siu Mui Tsai
- Cell and Molecular Biology Laboratory, Center for Nuclear Energy in Agriculture (CENA), University of Sao Paulo, Avenida Centenario 303, Piracicaba, Sao Paulo 13416-000, Brazil
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28
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Silva MOD, Pernthaler J. Biomass addition alters community assembly in ultrafiltration membrane biofilms. Sci Rep 2020; 10:11552. [PMID: 32665605 PMCID: PMC7360762 DOI: 10.1038/s41598-020-68460-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/15/2020] [Indexed: 11/25/2022] Open
Abstract
Freshwater biofilms assemble from a pool of rare water column genotypes. Random density fluctuations and temporal species turnover of functionally equivalent potential colonizers result in compositional variability of newly formed biofilm communities. We hypothesized that stronger environmental filtering as induced by enhanced substrate levels might reduce the impact of a locally variable pool of colonizers and instead select for more universal habitat specialists. Our model were heterotrophic biofilms that form on membranes during gravity-driven ultrafiltration of lake water. In four separate experiments, biomass of the cyanobacterium Microcystis was added to the feed water of one set of treatments (BM) and the resulting biofilm communities were compared to unamended controls (CTRL). Biomass addition led to a significant shift of community assembly processes: Replicate BM biofilms were more similar to each other than by chance in 3 of 4 experiments, whereas the opposite was the case for CTRL communities. Moreover, BM communities were more stochastically assembled across experiments from a common 'regional' pool of biofilm colonizers, whereas the composition of CTRL communities was mainly determined by experiment-specific 'local' genotypes. Interestingly, community assembly processes were also related to both, physiology (aerobic vs. anaerobic lifestyle) and the phylogenetic affiliation of biofilm bacteria.
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Affiliation(s)
- Marisa O D Silva
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland.
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29
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David AS, Thapa‐Magar KB, Menges ES, Searcy CA, Afkhami ME. Do plant–microbe interactions support the Stress Gradient Hypothesis? Ecology 2020; 101:e03081. [DOI: 10.1002/ecy.3081] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 02/15/2020] [Accepted: 03/18/2020] [Indexed: 12/19/2022]
Affiliation(s)
- Aaron S. David
- Department of Biology University of Miami 1301 Memorial Drive Coral Gables 33146 Florida USA
| | - Khum B. Thapa‐Magar
- Department of Biology University of Miami 1301 Memorial Drive Coral Gables 33146 Florida USA
| | - Eric S. Menges
- Archbold Biological Station 123 Main Drive Venus 33960 Florida USA
| | - Christopher A. Searcy
- Department of Biology University of Miami 1301 Memorial Drive Coral Gables 33146 Florida USA
| | - Michelle E. Afkhami
- Department of Biology University of Miami 1301 Memorial Drive Coral Gables 33146 Florida USA
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30
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Wisnoski NI, Muscarella ME, Larsen ML, Peralta AL, Lennon JT. Metabolic insight into bacterial community assembly across ecosystem boundaries. Ecology 2020; 101:e02968. [DOI: 10.1002/ecy.2968] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/14/2019] [Accepted: 12/20/2019] [Indexed: 12/23/2022]
Affiliation(s)
| | | | - Megan L. Larsen
- Department of Biology Indiana University Bloomington Indiana47405USA
| | - Ariane L. Peralta
- Department of Biology Indiana University Bloomington Indiana47405USA
| | - Jay T. Lennon
- Department of Biology Indiana University Bloomington Indiana47405USA
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31
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Aquatic Macrophytes and Local Factors Drive Bacterial Community Distribution and Interactions in a Riparian Zone of Lake Taihu. WATER 2020. [DOI: 10.3390/w12020432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Aquatic macrophytes rhizosphere are biogeochemical cycling hotspots in freshwater ecosystems. However, little is known regarding the effect of aquatic macrophytes on bacterial community and interactions in the riparian zones. We investigated the bacterial community composition and network structures along a gradient of the riparian zone as follows: The supralittoral and eulittoral zones with Phragmites australis, the eulittoral and infralittoral zones without P. australi. The bacterial communities in the four zones differed significantly based on taxonomic dissimilarity, but the two zones with P. australis exhibited phylogenetic closeness of the bacterial communities. The characteristics of the bacterial networks, such as connectivity, modularity, and topological roles of OTUs, were totally different between the P. australis and non-P. australis zones. Some bacterial phyla enriched in the P. australis zones were found to be putative keystone taxa in the networks, which might be involved in the regulation of bacterial interactions and plant growth. Moreover, the hydrological regime and particle size were shown to be determinants of the bacterial community and network structures in the riparian zones. In summary, our results show that the role of P. australis and local factors are crucial for constructing bacterial community and interactions in the riparian zones of lakes.
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32
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Morris MM, Frixione NJ, Burkert AC, Dinsdale EA, Vannette RL. Microbial abundance, composition, and function in nectar are shaped by flower visitor identity. FEMS Microbiol Ecol 2020; 96:5700281. [DOI: 10.1093/femsec/fiaa003] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 01/08/2020] [Indexed: 11/12/2022] Open
Abstract
ABSTRACT
Microbial dispersal is essential for establishment in new habitats, but the role of vector identity is poorly understood in community assembly and function. Here, we compared microbial assembly and function in floral nectar visited by legitimate pollinators (hummingbirds) and nectar robbers (carpenter bees). We assessed effects of visitation on the abundance and composition of culturable bacteria and fungi and their taxonomy and function using shotgun metagenomics and nectar chemistry. We also compared metagenome-assembled genomes (MAGs) of Acinetobacter, a common and highly abundant nectar bacterium, among visitor treatments. Visitation increased microbial abundance, but robbing resulted in 10× higher microbial abundance than pollination. Microbial communities differed among visitor treatments: robbed flowers were characterized by predominant nectar specialists within Acetobacteraceae and Metschnikowiaceae, with a concurrent loss of rare taxa, and these resulting communities harbored genes relating to osmotic stress, saccharide metabolism and specialized transporters. Gene differences were mirrored in function: robbed nectar contained a higher percentage of monosaccharides. Draft genomes of Acinetobacter revealed distinct amino acid and saccharide utilization pathways in strains isolated from robbed versus pollinated flowers. Our results suggest an unrecognized cost of nectar robbing for pollination and distinct effects of visitor type on interactions between plants and pollinators. Overall, these results suggest vector identity is an underappreciated factor structuring microbial community assembly and function.
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Affiliation(s)
- Megan M Morris
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Natalie J Frixione
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - Alexander C Burkert
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
| | | | - Rachel L Vannette
- Department of Entomology and Nematology, University of California, Davis, Davis, CA 95616, USA
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Yang J, Wang Y, Cui X, Xue K, Zhang Y, Yu Z. Habitat filtering shapes the differential structure of microbial communities in the Xilingol grassland. Sci Rep 2019; 9:19326. [PMID: 31852979 PMCID: PMC6920139 DOI: 10.1038/s41598-019-55940-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 12/04/2019] [Indexed: 02/07/2023] Open
Abstract
The spatial variability of microorganisms in grasslands can provide important insights regarding the biogeographic patterns of microbial communities. However, information regarding the degree of overlap and partitions of microbial communities across different habitats in grasslands is limited. This study investigated the microbial communities in three distinct habitats from Xilingol steppe grassland, i.e. animal excrement, phyllosphere, and soil samples, by Illumina MiSeq sequencing. All microbial community structures, i.e. for bacteria, archaea, and fungi, were significantly distinguished according to habitat. A high number of unique microorganisms but few coexisting microorganisms were detected, suggesting that the structure of microbial communities was mainly regulated by species selection and niche differentiation. However, the sequences of those limited coexisting microorganisms among the three different habitats accounted for over 60% of the total sequences, indicating their ability to adapt to variable environments. In addition, the biotic interactions among microorganisms based on a co-occurrence network analysis highlighted the importance of Microvirga, Blastococcus, RB41, Nitrospira, and four norank members of bacteria in connecting the different microbiomes. Collectively, the microbial communities in the Xilingol steppe grassland presented strong habitat preferences with a certain degree of dispersal and colonization potential to new habitats along the animal excrement- phyllosphere-soil gradient. This study provides the first detailed comparison of microbial communities in different habitats in a single grassland, and offers new insights into the biogeographic patterns of the microbial assemblages in grasslands.
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Affiliation(s)
- Jie Yang
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanfen Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaoyong Cui
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiming Zhang
- Beijing Municipal Ecological Environment Bureau, Beijing, 100048, China
| | - Zhisheng Yu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China. .,Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
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Succession of Microbial Decomposers Is Determined by Litter Type, but Site Conditions Drive Decomposition Rates. Appl Environ Microbiol 2019; 85:AEM.01760-19. [PMID: 31604765 DOI: 10.1128/aem.01760-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/03/2019] [Indexed: 12/31/2022] Open
Abstract
Soil microorganisms are diverse, although they share functions during the decomposition of organic matter. Thus, preferences for soil conditions and litter quality were explored to understand their niche partitioning. A 1-year-long litterbag transplant experiment evaluated how soil physicochemical traits of contrasting sites combined with chemically distinct litters of sedge (S), milkvetch (M) from a grassland, and beech (B) from forest site decomposition. Litter was assessed by mass loss; C, N, and P contents; and low-molecular-weight compounds. Decomposition was described by the succession of fungi, Actinobacteria, Alphaproteobacteria, and Firmicutes; bacterial diversity; and extracellular enzyme activities. The M litter decomposed faster at the nutrient-poor forest site, where the extracellular enzymes were more active, but microbial decomposers were not more abundant. Actinobacteria abundance was affected by site, while Firmicutes and fungi by litter type and Alphaproteobacteria by both factors. Actinobacteria were characterized as late-stage substrate generalists, while fungi were recognized as substrate specialists and site generalists, particularly in the grassland. Overall, soil conditions determined the decomposition rates in the grassland and forest, but successional patterns of the main decomposers (fungi and Actinobacteria) were determined by litter type. These results suggest that shifts in vegetation mostly affect microbial decomposer community composition.IMPORTANCE Anthropogenic disturbance may cause shifts in vegetation and alter the litter input. We studied the decomposition of different litter types under soil conditions of a nutrient-rich grassland and nutrient-poor forest to identify factors responsible for changes in the community structure and succession of microbial decomposers. This will help to predict the consequences of induced changes on the abundance and activity of microbial decomposers and recognize if the decomposition process and resulting quality and quantity of soil organic matter will be affected at various sites.
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Armeli Minicante S, Piredda R, Quero GM, Finotto S, Bernardi Aubry F, Bastianini M, Pugnetti A, Zingone A. Habitat Heterogeneity and Connectivity: Effects on the Planktonic Protist Community Structure at Two Adjacent Coastal Sites (the Lagoon and the Gulf of Venice, Northern Adriatic Sea, Italy) Revealed by Metabarcoding. Front Microbiol 2019; 10:2736. [PMID: 32038505 PMCID: PMC6988810 DOI: 10.3389/fmicb.2019.02736] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/11/2019] [Indexed: 11/28/2022] Open
Abstract
The Lagoon of Venice (LoV) and the Gulf of Venice (GoV), two adjacent coastal Long Term Ecological Research (LTER) sites in the northern Adriatic Sea, represent a transitional/marine coupled ecosystem under the influence of regional and local factors. In this study, these sites were sampled on four dates from April 2016 to February 2017 for environmental DNA and relevant abiotic variables, aiming to assess the relative importance of habitat heterogeneity and connectivity in structuring the protist community. High Throughput Sequencing of V4-18S rRNA gene from 56 samples collected at seven stations produced ca 6 million reads, grouped into 7,336 Operational Taxonomic Units (OTUs) at 97% similarity, which were affiliated to protists belonging to 34 taxonomic groups. The whole community was dominated by Bacillariophyta, especially in spring-summer in the LoV, and by Dinophyta, mainly in the GoV. Ciliophora, Syndiniales, and Cryptophyceae were the next more abundant groups. The community structure varied across the seasons and was different in the two ecosystems, which shared 96% of the reads but showed a high proportion of OTUs distributed preferentially in one of the two sites (specialists) and a different partitioning of trophic categories. GoV specialists were mainly Dinophyceae (>56%), followed by Syndiniales and Bacillariophyta, while the LoV specialists were distributed among several groups, including Bacillariophyta, Syndiniales, Ciliophora, Cryptophyceae, and Trebouxiophyceae. The main abiotic drivers of the differences between protist communities were salinity and temperature, which however explained a minor part of the variance (17%), pointing at a higher relevance of biotic factors and inter-taxa relationships. This was more evident in the LoV, where the network analysis highlighted a higher number of OTUs’ connections than in the GoV. Overall, the metabarcoding approach allowed to depict the composition of the whole protist community in the lagoon and adjacent coastal waters with high resolution, revealing many taxa so far not reported in the area. In addition, despite no clear barrier to dispersal processes, differences in the relative abundance and temporal variability of local protist communities indicate that environmental heterogeneity, in these adjacent and connected ecosystems, can be strong enough to allow for ecological segregation.
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Affiliation(s)
| | - Roberta Piredda
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Grazia Marina Quero
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Stefania Finotto
- Institute of Marine Sciences, National Research Council, Venice, Italy
| | | | - Mauro Bastianini
- Institute of Marine Sciences, National Research Council, Venice, Italy
| | | | - Adriana Zingone
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
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Ortiz‐Álvarez R, Cáliz J, Camarero L, Casamayor EO. Regional community assembly drivers and microbial environmental sources shaping bacterioplankton in an alpine lacustrine district (Pyrenees, Spain). Environ Microbiol 2019; 22:297-309. [DOI: 10.1111/1462-2920.14848] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 10/29/2019] [Indexed: 11/30/2022]
Affiliation(s)
- Rüdiger Ortiz‐Álvarez
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes (CEAB ‐ CSIC). C/Accés cala St Francesc n°14, E‐17300 Blanes Catalonia Spain
| | - Joan Cáliz
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes (CEAB ‐ CSIC). C/Accés cala St Francesc n°14, E‐17300 Blanes Catalonia Spain
| | - Lluís Camarero
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes (CEAB ‐ CSIC). C/Accés cala St Francesc n°14, E‐17300 Blanes Catalonia Spain
| | - Emilio O. Casamayor
- Integrative Freshwater Ecology Group, Center for Advanced Studies of Blanes (CEAB ‐ CSIC). C/Accés cala St Francesc n°14, E‐17300 Blanes Catalonia Spain
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Hou L, Mulla SI, Niño-Garcia JP, Ning D, Rashid A, Hu A, Yu CP. Deterministic and stochastic processes driving the shift in the prokaryotic community composition in wastewater treatment plants of a coastal Chinese city. Appl Microbiol Biotechnol 2019; 103:9155-9168. [DOI: 10.1007/s00253-019-10177-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/12/2019] [Accepted: 10/07/2019] [Indexed: 12/20/2022]
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Mery-Araya C, Lear G, Perez-Garcia O, Astudillo-Garcia C, Singhal N. Using carbon substrate as a selection pressure to enhance the potential of aerobic granular sludge microbial communities for removing contaminants of emerging concern. BIORESOURCE TECHNOLOGY 2019; 290:121705. [PMID: 31295574 DOI: 10.1016/j.biortech.2019.121705] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 06/20/2019] [Accepted: 06/26/2019] [Indexed: 06/09/2023]
Abstract
The ability of aerobic granular sludge (AGS) technology to biotransform contaminants of emerging concern (CECs) is largely unknown. AGS supplemented with either acetate, 2-propanol, glycerol, or a 1:1:1 mixture of all three, were cultivated to investigate the link between carbon supplements and biotransformation of six CECs. Carbon substrate had a significant effect on the microbial community composition, as assessed by 16S rRNA gene sequence analyses. Substrate degradation requiring a larger number of catabolic reactions (i.e., glycerol and the mix) was associated with greater microbial richness. The biotransformation of CECs was 45.9% greater in communities supplemented with glycerol (60.3 ± 30.2 µg L-1 VSS-1) compared to acetate (20.9 ± 29.7 µg L-1 VSS-1). Database surveys of metabolic reactions indicate that microbial communities supplemented with glycerol have the greatest capacity for the degradation of aromatic compounds, while those supplemented with acetate community have the lowest.
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Affiliation(s)
- Camila Mery-Araya
- Department of Civil and Environmental Engineering, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; Departamento de Ingeniería Química y Ambiental, Universidad Técnica Federico Santa María, P.O. Box 110-V, Valparaíso, Chile.
| | - Gavin Lear
- School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1010, New Zealand
| | - Octavio Perez-Garcia
- Department of Civil and Environmental Engineering, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Carmen Astudillo-Garcia
- Departamento de Ingeniería Química y Ambiental, Universidad Técnica Federico Santa María, P.O. Box 110-V, Valparaíso, Chile
| | - Naresh Singhal
- Department of Civil and Environmental Engineering, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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Distinct responses from bacterial, archaeal and fungal streambed communities to severe hydrological disturbances. Sci Rep 2019; 9:13506. [PMID: 31534180 PMCID: PMC6751160 DOI: 10.1038/s41598-019-49832-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 08/24/2019] [Indexed: 11/08/2022] Open
Abstract
Stream microbes that occur in the Mediterranean Basin have been shown to possess heightened sensitivity to intensified water stress attributed to climate change. Here, we investigate the effects of long-term drought (150 days), storms and rewetting (7 days) on the diversity and composition of archaea, bacteria and fungi inhabiting intermittent streambed sediment (surface and hyporheic) and buried leaves. Hydrological alterations modified the archaeal community composition more than the bacterial community composition, whereas fungi were the least affected. Throughout the experiment, archaeal communities colonizing sediments showed greater phylogenetic distances compared to those of bacteria and fungi, suggesting considerable adaptation to severe hydrological disturbances. The increase in the class abundances, such as those of Thermoplasmata within archaea and of Actinobacteria and Bacilli within bacteria, revealed signs of transitioning to a drought-favoured and soil-like community composition. Strikingly, we found that in comparison to the drying phase, water return (as sporadic storms and rewetting) led to larger shifts in the surface microbial community composition and diversity. In addition, microhabitat characteristics, such as the greater capacity of the hyporheic zone to maintain/conserve moisture, tended to modulate the ability of certain microbes (e.g., bacteria) to cope with severe hydrological disturbances.
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40
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Rinella MJ, Reinhart KO. Toward more robust plant-soil feedback research. Ecology 2019; 99:550-556. [PMID: 29345304 DOI: 10.1002/ecy.2146] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/22/2017] [Accepted: 12/20/2017] [Indexed: 01/27/2023]
Abstract
Understanding if and how plant-soil biota feedbacks (PSFs) shape plant communities has become a major research priority. In this paper, we draw on a recent, high-profile PSF study to illustrate that certain widely used experimental methods cannot reliably determine if PSFs occur. One problem involves gathering soil samples adjacent to multiple conditioning plants, mixing the samples and then growing phytometers in the mixtures to test for PSFs. This mixed soil approach does not establish that the conditioning plant being present caused the soil biota to be present, the first step of a PSF. Also, soil mixing approximates replacing raw data with averages prior to analysis, a move certain to generate falsely precise statistical estimates. False precision also results from sample sizes being artificially inflated when phytometers are misinterpreted as experimental units. Plant biomass ratios become another source of false precision when individual plant values contribute to multiple ratio observations. Any one of these common missteps can cause still living null hypotheses to be pronounced dead, and risks of this increase with numbers of missteps. If soil organisms truly structure plant communities, then null hypotheses indicating otherwise will not survive proper testing. We discuss conceptual, experimental and analytical refinements to facilitate accurate testing.
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Affiliation(s)
- Matthew J Rinella
- United States Department of Agriculture-Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, 243 Fort Keogh Road, Miles City, Montana, 59301, USA
| | - Kurt O Reinhart
- United States Department of Agriculture-Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, 243 Fort Keogh Road, Miles City, Montana, 59301, USA
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41
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Halophilic microbial community compositional shift after a rare rainfall in the Atacama Desert. ISME JOURNAL 2019; 13:2737-2749. [PMID: 31273300 PMCID: PMC6794293 DOI: 10.1038/s41396-019-0468-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 05/29/2019] [Accepted: 06/12/2019] [Indexed: 12/13/2022]
Abstract
Understanding the mechanisms underlying microbial resistance and resilience to perturbations is essential to predict the impact of climate change on Earth’s ecosystems. However, the resilience and adaptation mechanisms of microbial communities to natural perturbations remain relatively unexplored, particularly in extreme environments. The response of an extremophile community inhabiting halite (salt rocks) in the Atacama Desert to a catastrophic rainfall provided the opportunity to characterize and de-convolute the temporal response of a highly specialized community to a major disturbance. With shotgun metagenomic sequencing, we investigated the halite microbiome taxonomic composition and functional potential over a 4-year longitudinal study, uncovering the dynamics of the initial response and of the recovery of the community after a rainfall event. The observed changes can be recapitulated by two general modes of community shifts—a rapid Type 1 shift and a more gradual Type 2 adjustment. In the initial response, the community entered an unstable intermediate state after stochastic niche re-colonization, resulting in broad predicted protein adaptations to increased water availability. In contrast, during recovery, the community returned to its former functional potential by a gradual shift in abundances of the newly acquired taxa. The general characterization and proposed quantitation of these two modes of community response could potentially be applied to other ecosystems, providing a theoretical framework for prediction of taxonomic and functional flux following environmental changes.
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42
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Zhao P, Liu J, Jia T, Luo Z, Li C, Chai B. Assembly mechanisms of soil bacterial communities in subalpine coniferous forests on the Loess Plateau, China. J Microbiol 2019; 57:461-469. [PMID: 31079332 DOI: 10.1007/s12275-019-8373-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 11/30/2022]
Abstract
Microbial community assembly is affected by trade-offs between deterministic and stochastic processes. However, the mechanisms underlying the relative influences of the two processes remain elusive. This knowledge gap limits our ability to understand the effects of community assembly processes on microbial community structures and functions. To better understand community assembly mechanisms, the community dynamics of bacterial ecological groups were investigated based on niche breadths in 23 soil plots from subalpine coniferous forests on the Loess Plateau in Shanxi, China. Here, the overall community was divided into the ecological groups that corresponded to habitat generalists, 'other taxa' and specialists. Redundancy analysis based on Bray-Curtis distances (db-RDA) and multiple regression tree (MRT) analysis indicated that soil organic carbon (SOC) was a general descriptor that encompassed the environmental gradients by which the communities responded to, because it can explain more significant variations in community diversity patterns. The three ecological groups exhibited different niche optima and degrees of specialization (i.e., niche breadths) along the SOC gradient, suggesting the presence of a gradient in tolerance for environmental heterogeneity. The inferred community assembly processes varied along the SOC gradient, wherein a transition was observed from homogenizing dispersal to variable selection that reflects increasing deterministic processes. Moreover, the ecological groups were inferred to perform different community functions that varied with community composition, structure. In conclusion, these results contribute to our understanding of the trade-offs between community assembly mechanisms and the responses of community structure and function to environmental gradients.
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Affiliation(s)
- Pengyu Zhao
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, P. R. China
| | - Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, P. R. China
| | - Tong Jia
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, P. R. China
| | - Zhengming Luo
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, P. R. China
| | - Cui Li
- Faculty of Environment Economics, Shanxi University of Finance and Economics, Taiyuan, 030006, P. R. China
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, P. R. China.
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Muscarella ME, Boot CM, Broeckling CD, Lennon JT. Resource heterogeneity structures aquatic bacterial communities. ISME JOURNAL 2019; 13:2183-2195. [PMID: 31053829 DOI: 10.1038/s41396-019-0427-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 04/10/2019] [Indexed: 01/20/2023]
Abstract
Microorganisms are strongly influenced by the bottom-up effects of resource supply. While many species respond to fluctuations in the concentration of resources, microbial diversity may also be affected by the heterogeneity of the resource pool, which often reflects a mixture of distinct molecules. To test this hypothesis, we examined resource-diversity relationships for bacterioplankton in a set of north temperate lakes that varied in their concentration and composition of dissolved organic matter (DOM), which is an important resource for heterotrophic bacteria. Using 16S rRNA transcript sequencing and ecosystem metabolomics, we documented strong relationships between bacterial alpha-diversity (richness and evenness) and the bulk concentration and the number of molecules in the DOM pool. Similarly, bacterial community beta-diversity was related to both DOM concentration and composition. However, in some lakes the relative abundance of resource generalists, which was inversely related to the DOM concentration, may have reduced the effect of DOM heterogeneity on community composition. Together, our results demonstrate the potential metabolic interactions between bacteria and organic matter and suggest that changes in organic matter composition may alter the structure and function of bacterial communities.
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Affiliation(s)
- Mario E Muscarella
- Department of Plant Biology, University of Illinois, Urbana-Champaign, IL, 61801, USA.,Department of Biology, Indiana University, Bloomington, IN, 47405, USA
| | - Claudia M Boot
- Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, 80523, CO, USA.,Department of Chemistry, Colorado State University, Fort Collins, 80523, CO, USA
| | - Corey D Broeckling
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, 80523, CO, USA
| | - Jay T Lennon
- Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
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Silva MOD, Desmond P, Derlon N, Morgenroth E, Pernthaler J. Source Community and Assembly Processes Affect the Efficiency of Microbial Microcystin Degradation on Drinking Water Filtration Membranes. Front Microbiol 2019; 10:843. [PMID: 31057530 PMCID: PMC6482319 DOI: 10.3389/fmicb.2019.00843] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 04/02/2019] [Indexed: 01/14/2023] Open
Abstract
Microbial biofilms in gravity-driven membrane (GDM) filtration systems can efficiently degrade the cyanotoxin microcystin (MC), but it is unclear if this function depends on the presence of MC-producing cyanobacteria in the source water habitat. We assessed the removal of MC from added Microcystis aeruginosa biomass in GDMs fed with water from a lake with regular blooms of toxic cyanobacteria (ExpL) or from a stream without such background (ExpS). While initial MC removal was exclusively due to abiotic processes, significantly higher biological MC removal was observed in ExpL. By contrast, there was no difference in MC degradation capacity between lake and stream bacteria in separately conducted liquid enrichments on pure MC. Co-occurrence network analysis revealed a pronounced modularity of the biofilm communities, with a clear hierarchic distinction according to feed water origin and treatment type. Genotypes in the network modules associated with ExpS had significantly more links to each other, indicating that these biofilms had assembled from a more coherent source community. In turn, signals for stochastic community assembly were stronger in ExpL biofilms. We propose that the less "tightly knit" ExpL biofilm assemblages allowed for the better establishment of facultatively MC degrading bacteria, and thus for higher overall functional efficiency.
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Affiliation(s)
- Marisa O. D. Silva
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Peter Desmond
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Institute of Environmental Engineering, ETH Zurich, Institute of Environmental Engineering, Zurich, Switzerland
| | - Nicolas Derlon
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Eberhard Morgenroth
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
- Institute of Environmental Engineering, ETH Zurich, Institute of Environmental Engineering, Zurich, Switzerland
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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Hou L, Hu A, Chen S, Zhang K, Orlić S, Rashid A, Yu CP. Deciphering the Assembly Processes of the Key Ecological Assemblages of Microbial Communities in Thirteen Full-Scale Wastewater Treatment Plants. Microbes Environ 2019; 34:169-179. [PMID: 30996148 PMCID: PMC6594736 DOI: 10.1264/jsme2.me18107] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Limited information is currently available on the assembly processes (deterministic vs. stochastic) shaping the compositions of key microbial communities in activated sludge (AS). The relative importance of deterministic and stochastic processes for key bacterial and archaeal assemblages (i.e., core-satellite and habitat generalist-specialist) in AS from 13 wastewater treatment plants in China was investigated using 16S rDNA amplicon sequencing. The results obtained indicated 1,388 and 369 core operational taxonomic units (OTUs), 1,038 and 1,683 satellite OTUs, 255 and 48 habitat generalist OTUs, and 192 and 111 habitat specialist OTUs for Bacteria and Archaea, respectively. The proportions of shared OTUs between core and habitat specialist communities were similar to or higher than those between core and habitat generalist communities, suggesting a stronger inter-linkage between the former two groups. Deterministic processes, indicated by abundance-based β-null models, were responsible for shaping core communities, in which NH4-N, OrgC/OrgN, Cr, and Ni were the main controlling factors. In contrast, satellite communities were predominantly influenced by stochastic processes. Moreover, we found that deterministic and stochastic processes were mainly responsible for shaping the assembly of habitat specialists and generalists, respectively. However, the influence of deterministic factors on habitat specialists remains unclear. The present study provides novel insights into the assembly mechanisms of AS microbial communities.
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Affiliation(s)
- Liyuan Hou
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences.,Department of Civil and Environmental Engineering, University of Missouri
| | - Anyi Hu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences
| | - Shaohua Chen
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences
| | - Kaisong Zhang
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences
| | - Sandi Orlić
- Ruđer Bošković Institute.,Center of Excellence for Science and Technology-integration of Mediterranean region- STIM
| | - Azhar Rashid
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences.,Nuclear Institute for Food and Agriculture
| | - Chang-Ping Yu
- CAS Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences.,Graduate Institute of Environmental Engineering, National Taiwan University
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Luo Z, Liu J, Zhao P, Jia T, Li C, Chai B. Biogeographic Patterns and Assembly Mechanisms of Bacterial Communities Differ Between Habitat Generalists and Specialists Across Elevational Gradients. Front Microbiol 2019; 10:169. [PMID: 30804920 PMCID: PMC6378303 DOI: 10.3389/fmicb.2019.00169] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 01/22/2019] [Indexed: 11/29/2022] Open
Abstract
A core issue in microbial ecology is the need to elucidate the ecological processes and underlying mechanisms involved in microbial community assembly. However, the extent to which these mechanisms differ in importance based on traits of taxa with different niche breadth is poorly understood. Here, we used high-throughput sequencing to examine the relative importance of environmental selection and stochastic processes in shaping soil bacterial sub-communities with different niche breadth (including habitat generalists, specialists and other taxa) across elevational gradients on the subalpine slope of Mount Wutai, Northern China. Our findings suggested that the composition of soil bacterial communities differed significantly different among elevational gradients. According to the niche breadth index, 10.9% of OTUs were defined as habitat generalists (B-value >8.7) and 10.0% of OTUs were defined as habitat specialists (B-value <1.5). Generalists and specialists differed distinctly in diversity and biogeographic patterns across elevational gradients. Environmental selection (deterministic processes) and spatial factors (stochastic processes) seemed to determine the assembly and biogeography of habitat generalists. However, for specialists, deterministic processes strongly influenced the distribution, while stochastic processes were not at play. Environmental drivers for generalists and specialists differed, as did their importance. Elevation, total nitrogen and pH were the main factors determining habitat generalists, and soil water content, nitrate nitrogen and pH had the strongest impacts on specialists. Moreover, variation partitioning analysis revealed that environmental selection had a much greater impact on both generalists (17.7% of pure variance was explained) and specialists (3.6%) than spatial factors. However, generalists had a much stronger response to spatial factors (2.3%) than specialists (0.3%). More importantly, null models of β-diversity suggested that specialists deviated significantly from non-neutral assembly mechanisms (relative null deviation= 0.64–0.74) relative to generalists (0.16–0.65) (P < 0.05). These results indicate that generalists and specialists are governed by different assembly mechanisms and present distinct biogeographical patterns. The large proportion of unexplained variation in specialists (93.3%) implies that very complex assembly mechanisms exist in the assembly of specialists across elevational gradients on the subalpine slope of Mount Wutai. It is essential to understand the microbial community assembly at a more refined level, and to expand the current understanding of microbial ecological mechanisms.
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Affiliation(s)
- Zhengming Luo
- Institute of Loess Plateau, Shanxi University, Taiyuan, China.,Department of Geography, Xinzhou Teachers University, Xinzhou, China
| | - Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Pengyu Zhao
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Tong Jia
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
| | - Cui Li
- Department of Environment and Economics, Shanxi University of Finance and Economics, Taiyuan, China
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Taiyuan, China
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Guan Y, Jia J, Wu L, Xue X, Zhang G, Wang Z. Analysis of Bacterial Community Characteristics, Abundance of Antibiotics and Antibiotic Resistance Genes Along a Pollution Gradient of Ba River in Xi'an, China. Front Microbiol 2018; 9:3191. [PMID: 30619235 PMCID: PMC6308138 DOI: 10.3389/fmicb.2018.03191] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 12/10/2018] [Indexed: 12/26/2022] Open
Abstract
The microbial communities in freshwater have raised concerns about the ecosystem and human health. Many ecological environmental problems have been found in urban river because of the unreasonable use and long-term wastewater discharge. In this study, we explored the bacterial community composition, abundance of 14 antibiotics and 21 antibiotic resistance genes (ARGs), and water environment features in seven water samples and seven sediment samples from Ba River in Xi'an, China. Results showed Proteobacteria and Bacteroidetes were the dominant phyla in all samples, and sediment samples had a higher bacterial diversity and richness than it in water. Bacterial communities of site 5 and 6 were clustered in discrepant patterns compared to those at remaining sites from other samples. It might be influenced by nutrients, heavy metals and antibiotics. Antibiotics concentrations ranged from 1.26 to 1.61 × 103 ng L-1 in water samples and 1.55 to 4.05 × 102 μg kg-1 in sediment samples. Sulfamerazine (SM1) and erythromycin (ERY) were the chief antibiotics in water samples, while the level of oxytetracycline (OTC) and cefazolin (CFZ) were higher in sediment samples. Canonical correspondence analysis showed that trimethoprim (TMP) was significantly related to Acinetobacter in W6, and that SM1 and OTC had positive correlation with Arcobacter in W5. The tetC, blaTEM , ermF and sul1 had higher pollution abundance ranging from 10-4 to 100 copies/16S rRNA gene copies in all samples. Significant correlations were observed between ARGs and matching antibiotics, suggesting that antibiotics can pose the selective pressure on ARGs in this river. In summary, these finding might provide some new data to the limited information available on the bacterial community characteristics, abundance of antibiotics and ARGs in urban river of China.
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Affiliation(s)
- Yongjing Guan
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jia Jia
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Lang Wu
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xue Xue
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Guo Zhang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zaizhao Wang
- Shaanxi Key Laboratory of Molecular Biology for Agriculture, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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De Anda V, Zapata-Peñasco I, Blaz J, Poot-Hernández AC, Contreras-Moreira B, González-Laffitte M, Gámez-Tamariz N, Hernández-Rosales M, Eguiarte LE, Souza V. Understanding the Mechanisms Behind the Response to Environmental Perturbation in Microbial Mats: A Metagenomic-Network Based Approach. Front Microbiol 2018; 9:2606. [PMID: 30555424 PMCID: PMC6280815 DOI: 10.3389/fmicb.2018.02606] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 10/11/2018] [Indexed: 12/26/2022] Open
Abstract
To date, it remains unclear how anthropogenic perturbations influence the dynamics of microbial communities, what general patterns arise in response to disturbance, and whether it is possible to predict them. Here, we suggest the use of microbial mats as a model of study to reveal patterns that can illuminate the ecological processes underlying microbial dynamics in response to stress. We traced the responses to anthropogenic perturbation caused by water depletion in microbial mats from Cuatro Cienegas Basin (CCB), Mexico, by using a time-series spatially resolved analysis in a novel combination of three computational approaches. First, we implemented MEBS (Multi-genomic Entropy-Based Score) to evaluate the dynamics of major biogeochemical cycles across spatio-temporal scales with a single informative value. Second, we used robust Time Series-Ecological Networks (TS-ENs) to evaluate the total percentage of interactions at different taxonomic levels. Lastly, we utilized network motifs to characterize specific interaction patterns. Our results indicate that microbial mats from CCB contain an enormous taxonomic diversity with at least 100 phyla, mainly represented by members of the rare biosphere (RB). Statistical ecological analyses point out a clear involvement of anaerobic guilds related to sulfur and methane cycles during wet versus dry conditions, where we find an increase in fungi, photosynthetic, and halotolerant taxa. TS-ENs indicate that in wet conditions, there was an equilibrium between cooperation and competition (positive and negative relationships, respectively), while under dry conditions there is an over-representation of negative relationships. Furthermore, most of the keystone taxa of the TS-ENs at family level are members of the RB and the microbial mat core highlighting their crucial role within the community. Our results indicate that microbial mats are more robust to perturbation due to redundant functions that are likely shared among community members in the highly connected TS-ENs with density values close to one (≈0.9). Finally, we provide evidence that suggests that a large taxonomic diversity where all community members interact with each other (low modularity), the presence of permanent of low-abundant taxa, and an increase in competition can be potential buffers against environmental disturbance in microbial mats.
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Affiliation(s)
- Valerie De Anda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Icoquih Zapata-Peñasco
- Dirección de Investigación en Transformación de Hidrocarburos, Instituto Mexicano del Petróleo, Eje Central Lázaro Cárdenas, Ciudad de México, Mexico
| | - Jazmín Blaz
- Laboratorio Nacional de Ciencias de la Sostenibilidad, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Augusto Cesar Poot-Hernández
- Departamento de Ingeniería de Sistemas Computacionales y Automatización, Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, UNAM, Ciudad Universitaria, Ciudad de México, Mexico
| | - Bruno Contreras-Moreira
- Estación Experimental de Aula Dei, Consejo Superior de Investigaciones Científicas, Zaragoza, Spain
- Fundación ARAID, Zaragoza, Spain
| | | | - Niza Gámez-Tamariz
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Luis E. Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Valeria Souza
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Röhl O, Graupner N, Peršoh D, Kemler M, Mittelbach M, Boenigk J, Begerow D. Flooding Duration Affects the Structure of Terrestrial and Aquatic Microbial Eukaryotic Communities. MICROBIAL ECOLOGY 2018; 75:875-887. [PMID: 29026984 DOI: 10.1007/s00248-017-1085-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/29/2017] [Indexed: 05/22/2023]
Abstract
The increasing number and duration of inundations is reported to be a consequence of climate change and may severely compromise non-adapted macroorganisms. The effect of flooding events on terrestrial and aquatic microbial communities is, however, less well understood. They may respond to the changed abiotic properties of their native habitat, and the native community may change due to the introduction of alien species. We designed an experiment to investigate the effect of five different flooding durations on the terrestrial and aquatic communities of eukaryotic microorganism, using the AquaFlow mesocosms. With amplicon sequencing of the small subunit (SSU) and internal transcribed spacer (ITS) rRNA gene regions, we analyzed community compositions directly before and after flooding. Subsequently, they were monitored for another 28 days, to determine the sustainability of community changes. Our results revealed a temporary increase in similarity between terrestrial and aquatic communities according to OTU composition (operational taxonomic unit, serves as a proxy for species). Increased similarity was mainly caused by the transmission of OTUs from water to soil. A minority of these were able to persist in soil until the end of the experiment. By contrast, the vast majority of soil OTUs was not transmitted to water. Flooding duration affected the community structure (abundance) more than composition (occurrence). Terrestrial communities responded immediately to flooding and the flooding duration influenced the community changes. Independent from flooding duration, all terrestrial communities recovered largely after flooding, indicating a remarkable resilience to the applied disturbances. Aquatic communities responded immediately to the applied inundations too. At the end of the experiment, they grouped according to the applied flooding duration and the amount of ammonium and chloride that leached from the soil. This indicates a sustained long-term response of the aquatic communities to flooding events.
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Affiliation(s)
- Oliver Röhl
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
| | - Nadine Graupner
- Department of Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Derek Peršoh
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Martin Kemler
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Moritz Mittelbach
- AG Ökologie der Pflanzen; Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
| | - Jens Boenigk
- Department of Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Dominik Begerow
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
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50
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Lisa JA, Jayakumar A, Ward BB, Song B. nirS-type denitrifying bacterial assemblages respond to environmental conditions of a shallow estuary. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:766-778. [PMID: 28914491 DOI: 10.1111/1758-2229.12594] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 08/31/2017] [Accepted: 09/07/2017] [Indexed: 06/07/2023]
Abstract
Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered 'generalist' and 'specialist' archetypes based on the distribution of archetypes within these assemblages. Generalists, archetypes detected in all samples during at least one season, were commonly world-wide found in estuarine and marine ecosystems, comprised 8%-29% of the abundant NRE archetypes. Archetypes found in a particular site, 'specialists', were found to co-vary based on site specific conditions. Archetypes specific to the lower estuary in winter were designated Cluster I and significantly correlated by sediment Chl a and porewater Fe2+ . A combination of specialist and more widely distributed archetypes formed Clusters II and III, which separated based on salinity and porewater H2 S respectively. The co-occurrence of archetypes correlated with different environmental conditions highlights the importance of habitat type and niche differentiation among nirS-type denitrifying communities and supports the essential role of individual community members in overall ecosystem function.
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Affiliation(s)
- Jessica A Lisa
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & May, Gloucester Point, VA, USA
| | - Amal Jayakumar
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Bess B Ward
- Department of Geosciences, Princeton University, Princeton, NJ, USA
| | - Bongkeun Song
- Department of Biological Sciences, Virginia Institute of Marine Science, College of William & May, Gloucester Point, VA, USA
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