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Aguado-Santacruz GA, Arreola-Tostado JM, Aguirre-Mancilla C, García-Moya E. Use of systemic biofertilizers in sugarcane results in highly reproducible increments in yield and quality of harvests. Heliyon 2024; 10:e28750. [PMID: 38596061 PMCID: PMC11002039 DOI: 10.1016/j.heliyon.2024.e28750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 02/28/2024] [Accepted: 03/24/2024] [Indexed: 04/11/2024] Open
Abstract
The utilization of a novel (systemic) biofertilizer containing Pseudomonas fluorescens, Azospirillum brasilense, and Bacillus subtilis and possessing the technology to facilitate the entry of bacteria through the stomata, was evaluated at three localities in Mexico (Potrero Nuevo, Veracruz; Ameca, Jalisco; and Champotón, Campeche) in two sugarcane varieties (NCO-310 and Mex 57-473) at different time scales. Inoculation of the systemic biofertilizer was imposed over the local agricultural management of the sugarcane; chemical fertilization of the experimental parcels at Potrero Nuevo was done using 70-20-20 and 120-80-80 at Ameca and Champotón. Three doses of the biofertilizer per hectare were applied during the annual productive cycle of sugarcane at each site; one year at Potrero Nuevo and Champotón; and six years at Ameca. The annual sugarcane yield was evaluated at each site. Additionally, sugar quality (°Brix or sucrose content) was evaluated at the three localities, while different variables of stalk performance were also measured at Ameca and Champotón. Our data provide evidence that this systemic biofertilizer consistently and reliably increased the sugarcane yield at all localities during the time of evaluation, ranging from 73.7 tons ha-1 at Potrero Nuevo (2.5 times increase; P < 0.05) and 77.7 tons ha-1 at Ameca (1.9 times increase; P < 0.05) to 23.8 tons ha-1 at Champotón (1.4 times increase; P < 0.05). This increase in sugarcane biomass was related to increased tillering rather than increased stalk height or diameter. This novel biological product improved the sugarcane quality in terms of °Brix (P < 0.05, 2.6° difference) and sucrose content (P < 0.5, 0.7% difference).
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Affiliation(s)
- Gerardo Armando Aguado-Santacruz
- BIOqualitum. Oriente 7 # 158, Ciudad Industrial, Celaya, Guanajuato, 38010, Mexico
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias. Km 6.5 Carretera Celaya-San Miguel de Allende, Celaya, Guanajuato, 38110, Mexico
| | | | - César Aguirre-Mancilla
- Tecnológico Nacional de México / IT de Roque. Km 8 Carretera Celaya - Juventino Rosas, C.P. 38110, Celaya, Guanajuato, Mexico
| | - Edmundo García-Moya
- Colegio de Postgraduados, Postgrado en Botánica, Montecillo, Texcoco, Estado de México, Mexico
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Gupta VVSR, Tiedje JM. Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales. MLIFE 2024; 3:21-41. [PMID: 38827504 PMCID: PMC11139212 DOI: 10.1002/mlf2.12116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/05/2024] [Accepted: 02/05/2024] [Indexed: 06/04/2024]
Abstract
The incredibly complex soil microbial communities at small scales make their analysis and identification of reasons for the observed structures challenging. Microbial community structure is mainly a result of the inoculum (dispersal), the selective advantages of those organisms under the habitat-based environmental attributes, and the ability of those colonizers to sustain themselves over time. Since soil is protective, and its microbial inhabitants have long adapted to varied soil conditions, significant portions of the soil microbial community structure are likely stable. Hence, a substantial portion of the community will not correlate to often measured soil attributes. We suggest that the drivers be ranked on the basis of their importance to the fundamental needs of the microbes: (i) those that supply energy, i.e., organic carbon and electron acceptors; (ii) environmental effectors or stressors, i.e., pH, salt, drought, and toxic chemicals; (iii) macro-organism associations, i.e., plants and their seasonality, animals and their fecal matter, and soil fauna; and (iv) nutrients, in order, N, P, and probably of lesser importance, other micronutrients, and metals. The relevance of drivers also varies with spatial and time scales, for example, aggregate to field to regional, and persistent to dynamic populations to transcripts, and with the extent of phylogenetic difference, hence phenotypic differences in organismal groups. We present a summary matrix to provide guidance on which drivers are important for particular studies, with special emphasis on a wide range of spatial and temporal scales, and illustrate this with genomic and population (rRNA gene) data from selected studies.
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Affiliation(s)
| | - James M. Tiedje
- Centre for Microbial EcologyMichigan State UniversityEast LansingMichiganUSA
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3
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Power JF, Carere CR, Welford HE, Hudson DT, Lee KC, Moreau JW, Ettema TJG, Reysenbach AL, Lee CK, Colman DR, Boyd ES, Morgan XC, McDonald IR, Craig Cary S, Stott MB. A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand. Nat Commun 2024; 15:179. [PMID: 38167814 PMCID: PMC10762115 DOI: 10.1038/s41467-023-43960-2] [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: 04/18/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Allopatric speciation has been difficult to examine among microorganisms, with prior reports of endemism restricted to sub-genus level taxa. Previous microbial community analysis via 16S rRNA gene sequencing of 925 geothermal springs from the Taupō Volcanic Zone (TVZ), Aotearoa-New Zealand, revealed widespread distribution and abundance of a single bacterial genus across 686 of these ecosystems (pH 1.2-9.6 and 17.4-99.8 °C). Here, we present evidence to suggest that this genus, Venenivibrio (phylum Aquificota), is endemic to Aotearoa-New Zealand. A specific environmental niche that increases habitat isolation was identified, with maximal read abundance of Venenivibrio occurring at pH 4-6, 50-70 °C, and low oxidation-reduction potentials. This was further highlighted by genomic and culture-based analyses of the only characterised species for the genus, Venenivibrio stagnispumantis CP.B2T, which confirmed a chemolithoautotrophic metabolism dependent on hydrogen oxidation. While similarity between Venenivibrio populations illustrated that dispersal is not limited across the TVZ, extensive amplicon, metagenomic, and phylogenomic analyses of global microbial communities from DNA sequence databases indicates Venenivibrio is geographically restricted to the Aotearoa-New Zealand archipelago. We conclude that geographic isolation, complemented by physicochemical constraints, has resulted in the establishment of an endemic bacterial genus.
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Affiliation(s)
- Jean F Power
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - Carlo R Carere
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Holly E Welford
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand
| | - Daniel T Hudson
- Te Tari Moromoroiti me te Ārai Mate | Department of Microbiology and Immunology, Te Whare Wānanga o Ōtākou | University of Otago, Dunedin, 9054, Aotearoa New Zealand
| | - Kevin C Lee
- Te Kura Pūtaiao | School of Science, Te Wānanga Aronui o Tāmaki Makau Rau | Auckland University of Technology, Auckland, 1010, Aotearoa New Zealand
| | - John W Moreau
- School of Geographical & Earth Sciences, University of Glasgow, Glasgow, G12 8RZ, UK
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University & Research, 6708, WE, Wageningen, the Netherlands
| | | | - Charles K Lee
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - Daniel R Colman
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Eric S Boyd
- Department of Microbiology and Cell Biology, Montana State University, Bozeman, MT, 59717, USA
| | - Xochitl C Morgan
- Te Tari Moromoroiti me te Ārai Mate | Department of Microbiology and Immunology, Te Whare Wānanga o Ōtākou | University of Otago, Dunedin, 9054, Aotearoa New Zealand
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Ian R McDonald
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand
| | - S Craig Cary
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, 3240, Aotearoa New Zealand.
| | - Matthew B Stott
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, 8140, Aotearoa New Zealand.
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Santos-Medellín C, Blazewicz SJ, Pett-Ridge J, Firestone MK, Emerson JB. Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils. Nat Ecol Evol 2023; 7:1809-1822. [PMID: 37770548 DOI: 10.1038/s41559-023-02207-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 08/25/2023] [Indexed: 09/30/2023]
Abstract
As central members of soil trophic networks, viruses have the potential to drive substantial microbial mortality and nutrient turnover. Pinpointing viral contributions to terrestrial ecosystem processes remains a challenge, as temporal dynamics are difficult to unravel in the spatially and physicochemically heterogeneous soil environment. In Mediterranean grasslands, the first rainfall after seasonal drought provides an ecosystem reset, triggering microbial activity during a tractable window for capturing short-term dynamics. Here, we simulated precipitation in microcosms from four distinct dry grassland soils and generated 144 viromes, 84 metagenomes and 84 16S ribosomal RNA gene amplicon datasets to characterize viral, prokaryotic and relic DNA dynamics over 10 days. Vastly different viral communities in each soil followed remarkably similar successional trajectories. Wet-up triggered a significant increase in viral richness, followed by extensive compositional turnover. Temporal succession in prokaryotic communities was much less pronounced, perhaps suggesting differences in the scales of activity captured by viromes (representing recently produced, ephemeral viral particles) and total DNA. Still, differences in the relative abundances of Actinobacteria (enriched in dry soils) and Proteobacteria (enriched in wetted soils) matched those of their predicted phages, indicating viral predation of dominant bacterial taxa. Rewetting also rapidly depleted relic DNA, which subsequently reaccumulated, indicating substantial new microbial mortality in the days after wet-up, particularly of the taxa putatively under phage predation. Production of abundant, diverse viral particles via microbial host cell lysis appears to be a conserved feature of the early response to soil rewetting, and results suggest the potential for 'Cull-the-Winner' dynamics, whereby viruses infect and cull but do not decimate dominant host populations.
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Affiliation(s)
| | - Steven J Blazewicz
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life & Environmental Sciences Department, University of California, Merced, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Mary K Firestone
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA
| | - Joanne B Emerson
- Department of Plant Pathology, University of California, Davis, CA, USA.
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Nobarinezhad MH, Wallace LE. Fine-scale genetic structure in rhizosphere microbial communities associated with Chamaecrista fasciculata (Fabaceae). Ecol Evol 2023; 13:e10570. [PMID: 37753306 PMCID: PMC10518841 DOI: 10.1002/ece3.10570] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/27/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Soil microbiota of the rhizosphere are an important extension of the plant phenotype because they impact the health and fitness of host plants. The composition of these communities is expected to differ among host plants due to influence by host genotype. Given that many plant populations exhibit fine-scale genetic structure (SGS), associated microbial communities may also exhibit SGS. In this study, we tested this hypothesis using Chamaecrista fasciculata, a legume species that has previously been determined to have significant SGS. We collected genetic data from prokaryotic and fungal rhizosphere communities in association with 70 plants in an area of ~400 square meters to investigate the presence of SGS in microbial communities. Bacteria of Acidobacteria, Protobacteria, and Bacteroidetes and fungi of Basidiomycota, Ascomycota, and Mortierellomycota were dominant members of the rhizosphere. Although microbial alpha diversity did not differ significantly among plants hosts, we detected significant compositional differences among the microbial communities as well as isolation by distance. The strongest factor associated with microbial distance was genetic distance of the other microbial community, followed by geographic distance, but there was not a significant association with plant genetic distance for either microbial community. This study further demonstrates the strong potential for spatial structuring of soil microbial communities at the smallest spatial scales and provides further insight into the complexity of factors that influence microbial composition in soils and in association with host plants.
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Affiliation(s)
| | - Lisa E. Wallace
- Department of Biological SciencesOld Dominion UniversityNorfolkVirginiaUSA
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Vigneron A, Vincent WF, Lovejoy C. Discovery of a novel bacterial class with the capacity to drive sulfur cycling and microbiome structure in a paleo-ocean analog. ISME COMMUNICATIONS 2023; 3:82. [PMID: 37596370 PMCID: PMC10439189 DOI: 10.1038/s43705-023-00287-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/21/2023] [Accepted: 07/26/2023] [Indexed: 08/20/2023]
Abstract
Uncultivated microbial taxa represent a large fraction of global microbial diversity and likely drive numerous biogeochemical transformations in natural ecosystems. Geographically isolated, polar ecosystems are complex microbial biomes and refuges of underexplored taxonomic and functional biodiversity. Combining amplicon sequencing with genome-centric metagenomic analysis of samples from one of the world's northernmost lakes (Lake A, Ellesmere Island, Canadian High Arctic), we identified a novel bacterial taxon that dominates in the bottom layer of anoxic, sulfidic, relict sea water that was isolated from the Arctic Ocean some 3000 years ago. Based on phylogenomic comparative analyses, we propose that these bacteria represent a new Class within the poorly described Electryoneota/AABM5-125-24 candidate phylum. This novel class, for which we propose the name Tariuqbacteria, may be either a relict of ancient ocean conditions or endemic to this High Arctic system, provisionally providing a rare example of high-taxonomy level endemism. Consistent with the geochemistry of the bottom water, the genetic composition of the Candidatus Tariuqbacter genome revealed a strictly anaerobic lifestyle with the potential for sulfate and sulfur reduction, a versatile carbon metabolism and the capability to eliminate competing bacteria through methylarsenite production, suggesting an allelochemical influence on microbiome structure by this planktonic microbe.
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Affiliation(s)
- Adrien Vigneron
- Département de Biologie, Université Laval, Québec, QC, Canada.
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, Canada.
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada.
- Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada.
| | - Warwick F Vincent
- Département de Biologie, Université Laval, Québec, QC, Canada
- Centre d'études nordiques (CEN), Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada
| | - Connie Lovejoy
- Département de Biologie, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
- Takuvik Joint International Laboratory, Université Laval, Québec, QC, Canada
- Québec Océan, Université Laval, Québec, QC, Canada
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7
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Kang Y, Wu H, Zhang Y, Wu Q, Guan Q, Lu K, Lin Y. Differential distribution patterns and assembly processes of soil microbial communities under contrasting vegetation types at distinctive altitudes in the Changbai Mountain. Front Microbiol 2023; 14:1152818. [PMID: 37333641 PMCID: PMC10272400 DOI: 10.3389/fmicb.2023.1152818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/29/2023] [Indexed: 06/20/2023] Open
Abstract
Diversity patterns and community assembly of soil microorganisms are essential for understanding soil biodiversity and ecosystem processes. Investigating the impacts of environmental factors on microbial community assembly is crucial for comprehending the functions of microbial biodiversity and ecosystem processes. However, these issues remain insufficiently investigated in related studies despite their fundamental significance. The present study aimed to assess the diversity and assembly of soil bacterial and fungal communities to altitude and soil depth variations in mountain ecosystems by using 16S and ITS rRNA gene sequence analyses. In addition, the major roles of environmental factors in determining soil microbial communities and assembly processes were further investigated. The results showed a U-shaped pattern of the soil bacterial diversity at 0-10 cm soil depth along altitudes, reaching a minimum value at 1800 m, while the fungal diversity exhibited a monotonically decreasing trend with increasing altitude. At 10-20 cm soil depth, the soil bacterial diversity showed no apparent changes along altitudinal gradients, while the fungal Chao1 and phylogenetic diversity (PD) indices exhibited hump-shaped patterns with increasing altitude, reaching a maximum value at 1200 m. Soil bacterial and fungal communities were distinctively distributed with altitude at the same depth of soil, and the spatial turnover rates in fungi was greater than in bacteria. Mantel tests suggested soil physiochemical and climate variables significantly correlated with the β diversity of microbial community at two soil depths, suggesting both soil and climate heterogeneity contributed to the variation of bacterial and fungal community. Correspondingly, a novel phylogenetic null model analysis demonstrated that the community assembly of soil bacterial and fungal communities were dominated by deterministic and stochastic processes, respectively. The assembly processes of bacterial community were significantly related to the soil DOC and C:N ratio, while the fungal community assembly processes were significantly related to the soil C:N ratio. Our results provide a new perspective to assess the responses of soil microbial communities to variations with altitude and soil depth.
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Affiliation(s)
- Yujuan Kang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Haitao Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yifan Zhang
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Tourism and Geography Sciences, Jilin Normal University, Siping, China
| | - Qiong Wu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Tourism and Geography Sciences, Jilin Normal University, Siping, China
| | - Qiang Guan
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Kangle Lu
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Yiling Lin
- Key Laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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Papudeshi B, Rusch DB, VanInsberghe D, Lively CM, Edwards RA, Bashey F. Host Association and Spatial Proximity Shape but Do Not Constrain Population Structure in the Mutualistic Symbiont Xenorhabdus bovienii. mBio 2023:e0043423. [PMID: 37154562 DOI: 10.1128/mbio.00434-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023] Open
Abstract
To what extent are generalist species cohesive evolutionary units rather than a compilation of recently diverged lineages? We examine this question in the context of host specificity and geographic structure in the insect pathogen and nematode mutualist Xenorhabdus bovienii. This bacterial species partners with multiple nematode species across two clades in the genus Steinernema. We sequenced the genomes of 42 X. bovienii strains isolated from four different nematode species and three field sites within a 240-km2 region and compared them to globally available reference genomes. We hypothesized that X. bovienii would comprise several host-specific lineages, such that bacterial and nematode phylogenies would be largely congruent. Alternatively, we hypothesized that spatial proximity might be a dominant signal, as increasing geographic distance might lower shared selective pressures and opportunities for gene flow. We found partial support for both hypotheses. Isolates clustered largely by nematode host species but did not strictly match the nematode phylogeny, indicating that shifts in symbiont associations across nematode species and clades have occurred. Furthermore, both genetic similarity and gene flow decreased with geographic distance across nematode species, suggesting differentiation and constraints on gene flow across both factors, although no absolute barriers to gene flow were observed across the regional isolates. Several genes associated with biotic interactions were found to be undergoing selective sweeps within this regional population. The interactions included several insect toxins and genes implicated in microbial competition. Thus, gene flow maintains cohesiveness across host associations in this symbiont and may facilitate adaptive responses to a multipartite selective environment. IMPORTANCE Microbial populations and species are notoriously hard to delineate. We used a population genomics approach to examine the population structure and the spatial scale of gene flow in Xenorhabdus bovienii, an intriguing species that is both a specialized mutualistic symbiont of nematodes and a broadly virulent insect pathogen. We found a strong signature of nematode host association, as well as evidence for gene flow connecting isolates associated with different nematode host species and collected from distinct study sites. Furthermore, we saw signatures of selective sweeps for genes involved with nematode host associations, insect pathogenicity, and microbial competition. Thus, X. bovienii exemplifies the growing consensus that recombination not only maintains cohesion but can also allow the spread of niche-beneficial alleles.
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Affiliation(s)
- Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, Australia
- National Centre for Genome Analysis Support, Pervasive Institute of Technology, Indiana University, Bloomington, Indiana, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, Indiana, USA
| | | | - Curtis M Lively
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Robert A Edwards
- Flinders Accelerator for Microbiome Exploration, Flinders University, Adelaide, Australia
| | - Farrah Bashey
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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9
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Barbour KM, Barrón-Sandoval A, Walters KE, Martiny JBH. Towards quantifying microbial dispersal in the environment. Environ Microbiol 2023; 25:137-142. [PMID: 36308707 PMCID: PMC10100412 DOI: 10.1111/1462-2920.16270] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 10/28/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Kristin M Barbour
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, USA
| | - Alberto Barrón-Sandoval
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, USA
| | | | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California-Irvine, Irvine, California, USA
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Endophytic Pseudomonas sp. from Agave palmeri Participate in the Rhizophagy Cycle and Act as Biostimulants in Crop Plants. BIOLOGY 2022; 11:biology11121790. [PMID: 36552299 PMCID: PMC9775861 DOI: 10.3390/biology11121790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/13/2022]
Abstract
Plant growth-promoting bacteria are generating increasing interest in the agricultural industry as a promising alternative to traditional chemical fertilizers; however, much of the focus has been on rhizosphere bacteria. Bacterial endophytes are another promising source of plant growth-promoting bacteria, and though many plants have already been prospected for beneficial microbes, desert plants have been underrepresented in such studies. In this study, we show the growth-promoting potential of five strains of endophytic Pseudomonas sp. isolated from Agave palmeri, an agave from the Sonoran Desert. When inoculated onto Kentucky bluegrass, clover, carrot, coriander, and wheat, endophytic Pseudomonas sp. increased seedling root lengths in all hosts and seedling shoot lengths in Kentucky bluegrass, carrot, and wheat. Transformation of the Pseudomonas sp. strain P3AW to express the fluorescent protein mCherry revealed that Pseudomonas sp. becomes endophytic in non-native hosts and participates in parts of the rhizophagy cycle, a process by which endophytic bacteria cycle between the soil and roots, bringing in nutrients from the soil which are then extracted through reactive oxygen-mediated bacterial degradation in the roots. Tracking of the Pseudomonas sp. strain P3AW also provided evidence for a system of endophyte, or endophyte cell content, transport via the vascular bundle. These results provide further evidence of the rhizophagy cycle in plants and how it relates to growth promotion in plants by biostimulant bacteria.
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11
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France MT, Brown SE, Rompalo AM, Brotman RM, Ravel J. Identification of shared bacterial strains in the vaginal microbiota of related and unrelated reproductive-age mothers and daughters using genome-resolved metagenomics. PLoS One 2022; 17:e0275908. [PMID: 36288274 PMCID: PMC9604009 DOI: 10.1371/journal.pone.0275908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/26/2022] [Indexed: 11/29/2022] Open
Abstract
It has been suggested that the human microbiome might be vertically transmitted from mother to offspring and that early colonizers may play a critical role in development of the immune system. Studies have shown limited support for the vertical transmission of the intestinal microbiota but the derivation of the vaginal microbiota remains largely unknown. Although the vaginal microbiota of children and reproductive age women differ in composition, the vaginal microbiota could be vertically transmitted. To determine whether there was any support for this hypothesis, we examined the vaginal microbiota of daughter-mother pairs from the Baltimore metropolitan area (ages 14-27, 32-51; n = 39). We assessed whether the daughter's microbiota was similar in composition to their mother's using metataxonomics. Permutation tests revealed that while some pairs did have similar vaginal microbiota, the degree of similarity did not exceed that expected by chance. Genome-resolved metagenomics was used to identify shared bacterial strains in a subset of the families (n = 22). We found a small number of bacterial strains that were shared between mother-daughter pairs but identified more shared strains between individuals from different families, indicating that vaginal bacteria may display biogeographic patterns. Earlier-in-life studies are needed to demonstrate vertical transmission of the vaginal microbiota.
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Affiliation(s)
- Michael T. France
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Sarah E. Brown
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Anne M. Rompalo
- Division of Infectious Diseases, John Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Rebecca M. Brotman
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
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Wang Y, Tian S, Wu N, Liu W, Li L, Wang X. Differential Microbial Communities in Paddy Soils Between Guiyang Plateaus and Chengdu Basins Drive the Incidence of Rice Bacterial Diseases. PLANT DISEASE 2022; 106:1882-1889. [PMID: 35021874 DOI: 10.1094/pdis-09-21-1974-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Southwest China has the most complex rice-growing regions in China. With great differences in topography, consisting mainly of basins and plateaus, ecological factors differ greatly between regions. In this study, bulk paddy soils collected from long-term rice fields in Chengdu (basins) and Guiyang (plateaus) were used to study the correlation between microbial diversity and the incidence of rice bacterial diseases. Results showed that the microbial community composition in paddy soils and the microbial functional categories differed significantly between basins and plateaus. They shared >70% of the dominant genera (abundance >1%), but the abundance of the dominant genera differed significantly. Functional analysis found that bulk paddy soils from Chengdu were significantly enriched in virulence factor-related genes; soils from Guiyang were enriched in biosynthesis of secondary metabolites, especially antibiotics. Correspondingly, Chengdu was significantly enriched in leaf bacterial pathogens Acidovorax, Xanthomonas, and Pseudomonas. Greenhouse experiments and correlation analysis showed that soil chemical properties had a greater effect on microbial community composition and positively correlated with the higher incidence of rice bacterial foot rot in Guiyang, whereas temperature had a greater effect on soil microbial functions and positively correlated with the higher severity index of leaf bacterial diseases in Chengdu. Our results provide a new perspective on how differences in microbial communities in paddy soils can influence the incidence of rice bacterial diseases in areas with different topographies.
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Affiliation(s)
- Yajiao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Institute of Plant Protection, Hebei Academy of Agricultural and Forestry Sciences, Baoding 071000, China
| | - Shuping Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Nan Wu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Wenwen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Li Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xifeng Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Maturana-Martínez C, Iriarte JL, Ha SY, Lee B, Ahn IY, Vernet M, Cape M, Fernández C, González HE, Galand PE. Biogeography of Southern Ocean Active Prokaryotic Communities Over a Large Spatial Scale. Front Microbiol 2022; 13:862812. [PMID: 35592001 PMCID: PMC9111744 DOI: 10.3389/fmicb.2022.862812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/18/2022] [Indexed: 12/04/2022] Open
Abstract
The activity of marine microorganisms depends on community composition, yet, in some oceans, less is known about the environmental and ecological processes that structure their distribution. The objective of this study was to test the effect of geographical distance and environmental parameters on prokaryotic community structure in the Southern Ocean (SO). We described the total (16S rRNA gene) and the active fraction (16S rRNA-based) of surface microbial communities over a ~6,500 km longitudinal transect in the SO. We found that the community composition of the total fraction was different from the active fraction across the zones investigated. In addition, higher α-diversity and stronger species turnover were displayed in the active community compared to the total community. Oceanospirillales, Alteromonadales, Rhodobacterales, and Flavobacteriales dominated the composition of the bacterioplankton communities; however, there were marked differences at the order level. Temperature, salinity, silicic acid, particulate organic nitrogen, and particulate organic carbon correlated with the composition of bacterioplankton communities. A strong distance–decay pattern between closer and distant communities was observed. We hypothesize that it was related to the different oceanic fronts present in the Antarctic Circumpolar Current. Our findings contribute to a better understanding of the complex arrangement that shapes the structure of bacterioplankton communities in the SO.
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Affiliation(s)
- Claudia Maturana-Martínez
- Centro de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL) and Universidad Austral de Chile, Valdivia, Chile.,Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, Banyuls-sur-Mer, France
| | - José Luis Iriarte
- Centro de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL) and Universidad Austral de Chile, Valdivia, Chile
| | - Sun-Yong Ha
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Boyeon Lee
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - In-Young Ahn
- Division of Polar Ocean Science, Korea Polar Research Institute, Incheon, South Korea
| | - Maria Vernet
- Scripps Institution of Oceanography, University of California, San Diego, San Diego, CA, United States
| | - Mattias Cape
- School of Oceanography, University of Washington, Seattle, WA, United States
| | - Camila Fernández
- Sorbonne Université, CNRS, Laboratoire d'Océanographie Microbienne (LOMIC), Banyuls-sur-Mer, France
| | - Humberto E González
- Centro de Investigación Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL) and Universidad Austral de Chile, Valdivia, Chile
| | - Pierre E Galand
- Sorbonne Université, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques, Banyuls-sur-Mer, France
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14
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Zhang B, Xue K, Zhou S, Wang K, Liu W, Xu C, Cui L, Li L, Ran Q, Wang Z, Hu R, Hao Y, Cui X, Wang Y. Environmental selection overturns the decay relationship of soil prokaryotic community over geographic distance across grassland biotas. eLife 2022; 11:70164. [PMID: 35073255 PMCID: PMC8828049 DOI: 10.7554/elife.70164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/21/2022] [Indexed: 11/26/2022] Open
Abstract
Though being fundamental to global diversity distribution, little is known about the geographic pattern of soil microorganisms across different biotas on a large scale. Here, we investigated soil prokaryotic communities from Chinese northern grasslands on a scale up to 4000 km in both alpine and temperate biotas. Prokaryotic similarities increased over geographic distance after tipping points of 1760–1920 km, generating a significant U-shape pattern. Such pattern was likely due to decreased disparities in environmental heterogeneity over geographic distance when across biotas, supported by three lines of evidences: (1) prokaryotic similarities still decreased with the environmental distance, (2) environmental selection dominated prokaryotic assembly, and (3) short-term environmental heterogeneity followed the U-shape pattern spatially, especially attributed to dissolved nutrients. In sum, these results demonstrate that environmental selection overwhelmed the geographic ‘distance’ effect when across biotas, overturning the previously well-accepted geographic pattern for microbes on a large scale.
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Affiliation(s)
- Biao Zhang
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Kai Xue
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Shutong Zhou
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Kui Wang
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Wenjing Liu
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Cong Xu
- Aerospace Information Research Institute, University of Chinese Academy of Sciences
| | - Lizhen Cui
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Linfeng Li
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Qinwei Ran
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Zongsong Wang
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Ronghai Hu
- College of Resources and Environment, University of Chinese Academy of Sciences
| | - Yanbin Hao
- College of Life Sciences, University of Chinese Academy of Sciences
| | - Xiaoyong Cui
- Key Laboratory of Adaptation and Evolution of Plateau Biota, University of Chinese Academy of Sciences
| | - Yanfen Wang
- College of Resources and Environment, University of Chinese Academy of Sciences
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15
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Hussain S, Liu H, Liu S, Yin Y, Yuan Z, Zhao Y, Cao H. Distribution and Assembly Processes of Soil Fungal Communities along an Altitudinal Gradient in Tibetan Plateau. J Fungi (Basel) 2021; 7:jof7121082. [PMID: 34947064 PMCID: PMC8706254 DOI: 10.3390/jof7121082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 12/25/2022] Open
Abstract
In soil ecosystems, fungi exhibit diverse biodiversity and play an essential role in soil biogeochemical cycling. Fungal diversity and assembly processes across soil strata along altitudinal gradients are still unclear. In this study, we investigated the structure and abundance of soil fungal communities among soil strata and elevational gradients on the Tibetan Plateau using Illumina MiSeq sequencing of internal transcribed spacer1 (ITS1). The contribution of neutral and niche ecological processes were quantified using a neutral community model and a null model-based methodology. Our results showed that fungal gene abundance increased along altitudinal gradients, while decreasing across soil strata. Along with altitudinal gradients, fungal α-diversity (richness) decreased from surface to deeper soil layers, while β-diversity showed weak correlations with elevations. The neutral community model showed an excellent fit for neutral processes and the lowest migration rate (R2 = 0.75). The null model showed that stochastic processes dominate in all samples (95.55%), dispersal limitations were dominated at the surface layer and decreased significantly with soil strata, while undominated processes (ecological drift) show a contrary trend. The log-normal model and the null model (βNTI) correlation analysis also neglect the role of niche-based processes. We conclude that stochastic dispersal limitations, together with ecological drifts, drive fungal communities.
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Affiliation(s)
- Sarfraz Hussain
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Hao Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Senlin Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Yifan Yin
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Zhongyuan Yuan
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
| | - Yuguo Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China;
| | - Hui Cao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture and Rural Affairs, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China; (S.H.); (H.L.); (S.L.); (Y.Y.); (Z.Y.)
- Correspondence:
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16
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Yang Y, Shi Y, Kerfahi D, Ogwu MC, Wang J, Dong K, Takahashi K, Moroenyane I, Adams JM. Elevation-related climate trends dominate fungal co-occurrence network structure and the abundance of keystone taxa on Mt. Norikura, Japan. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149368. [PMID: 34352461 DOI: 10.1016/j.scitotenv.2021.149368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/15/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Soil fungi play an important role in promoting nutrient cycling and maintaining ecosystem stability. Yet, there has been little understanding of how fungal co-occurrence networks differ along elevational climate gradients, a topic of interest to both macroecology and climate change studies. Based on high-throughput sequencing technology, we investigated the trend in co-occurrence network structure of soil fungal communities at 11 elevation levels along a 2300 m elevation gradient on Mt. Norikura, Japan, and identified the keystone taxa in the network, hypothesizing a progressive decline in network connectivity with elevation due to decreased plant diversity and enhanced environmental stress caused by changes in climate and soil characteristics. Our results demonstrated that network-level topological features such as network size, average degree, clustering coefficient, and modularity decreased significantly with increasing elevation, indicating that the fungal OTUs at low elevation were more closely associated and the network structure was more compact at low elevations. This conclusion was verified by the negative correlation between positive cohesion, negative cohesion and elevation. Moreover, the negative/positive cohesion ratio reached its peak value in mid-elevations with moderate environmental stress, indicating that the fungal community structure in mid-elevations was more stable than that at other elevations. We also found that the keystone taxa were more abundant at lower elevations. Furthermore, statistical analysis revealed that against a background of uniform geology, climate may play a dominant role in determining the properties and intensity of soil fungal networks, and significantly affect the abundance distribution of keystone taxa. These findings enhance understanding of the pattern and mechanism of the fungal community co-occurrence network along elevation, as well as the responses of microorganisms to climate change on a vertical scale in montane ecosystems. IMPORTANCE: Exploration of the elevational distribution of microbial networks and their driving factors and mechanisms may provide opportunities for predicting potential impacts of environmental changes, on ecosystem functions and biogeographic patterns at a broad scale. Although many studies have explored patterns of fungal community diversity and composition along various environmental gradients, it is unclear how the topological structure of co-occurrence networks shifts along elevational temperature gradients. In this study, we found that the connectivity of the fungal community decreased with increasing elevation and that climate was the dominant factor regulating co-occurrence patterns, apparently acting indirectly through soil characteristics. Our results also suggest that higher elevations on mountains have fewer keystone taxa than low elevations. These patterns may be related to the decrease of plant diversity and the increase of environmental stress along elevation gradients.
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Affiliation(s)
- Ying Yang
- School of Geography and Oceanography, Nanjing University, Nanjing, China
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Henan, China
| | - Dorsaf Kerfahi
- School of Natural Sciences, Department of Biological Sciences, Keimyung University, Daegu, Republic of Korea
| | - Matthew C Ogwu
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Marche - Floristic Research Center of the Apennines, Gran Sasso and Monti della Laga National Park, San Colombo, Barisciano, L'Aquila, Italy
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ke Dong
- Life Science Major, Kyonggi University, Suwon, South Korea
| | - Koichi Takahashi
- Department of Biological Sciences, Shinsu University, Matsumoto, Japan
| | - Itumeleng Moroenyane
- Institut National Recherche Scientifique Centre, Institut Armand Frappier Santé Biotechnologie, Quebéc, Canada
| | - Jonathan M Adams
- School of Geography and Oceanography, Nanjing University, Nanjing, China.
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17
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Wang Y, Lu G, Yu H, Du X, He Q, Yao S, Zhao L, Huang C, Wen X, Deng Y. Meadow degradation increases spatial turnover rates of the fungal community through both niche selection and dispersal limitation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 798:149362. [PMID: 34375268 DOI: 10.1016/j.scitotenv.2021.149362] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 07/08/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
The alpine meadow ecosystem, as the main ecosystem of the Qinghai-Tibet Plateau, has been heavily degraded over the past several decades due to overgrazing and climate change. Although soil microorganisms play key roles in the stability and succession of grassland ecosystems, their response to grassland degradation has not been investigated at spatial scale. Here, we systematically analyzed the spatial turnover rates of soil prokaryotic and fungal communities in degraded and undegraded meadows through distance-decay relationship (DDR) and species area relationship (SAR), as well as the community assembly mechanisms behind them. Although the composition and structure of both fungal and prokaryotic communities showed significant changes between undegraded and degraded meadows, steeper spatial turnover rates were only observed in fungi (Degraded Alpine Meadow β = 0.0142, Undegraded Alpine Meadow β = 0.0077, P < 0.05). Mantel tests indicated that edaphic variables and vegetation factors showed significant correlations to the β diversity of fungal community only in degraded meadow, suggesting soil and vegetation heterogeneity both contributed to the variation of fungal community in that system. Correspondingly, a novel phylogenetic null model analysis demonstrated that environmental selection was enhanced in the fungal community assembly process during meadow degradation. Interestingly, dispersal limitation was also enhanced for the fungal community in the degraded meadow, and its relative contribution to other assembly process (i.e. selection and drift) showed a significant linear increase with spatial distance, suggesting that dispersal limitation played a greater role as distance increased. Our findings indicated the spatial scaling of the fungal community is altered during meadow degradation by both niche selection and dispersal limitation. This study provides a new perspective for the assessment of soil microbial responses to vegetation changes in alpine areas.
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Affiliation(s)
- Yingcheng Wang
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China; CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China
| | - Guangxin Lu
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Hao Yu
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Environmental Science and Engineering, Liaoning Technical University, Fuxin 123000, China
| | - Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Qing He
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Shiting Yao
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Lirong Zhao
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Caixia Huang
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Xiaocheng Wen
- Collage of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (CAS), Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China.
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18
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Kiel Reese B, Sobol MS, Bowles MW, Hinrichs KU. Redefining the Subsurface Biosphere: Characterization of Fungi Isolated From Energy-Limited Marine Deep Subsurface Sediment. FRONTIERS IN FUNGAL BIOLOGY 2021; 2:727543. [PMID: 37744089 PMCID: PMC10512353 DOI: 10.3389/ffunb.2021.727543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/24/2021] [Indexed: 09/26/2023]
Abstract
The characterization of metabolically active fungal isolates within the deep marine subsurface will alter current ecosystem models and living biomass estimates that are limited to bacterial and archaeal populations. Although marine fungi have been studied for over fifty years, a detailed description of fungal populations within the deep subsurface is lacking. Fungi possess metabolic pathways capable of utilizing previously considered non-bioavailable energy reserves. Therefore, metabolically active fungi would occupy a unique niche within subsurface ecosystems, with the potential to provide an organic carbon source for heterotrophic prokaryotic populations from the transformation of non-bioavailable energy into substrates, as well as from the fungal necromass itself. These organic carbon sources are not currently being considered in subsurface energy budgets. Sediments from South Pacific Gyre subsurface, one of the most energy-limited environments on Earth, were collected during the Integrated Ocean Drilling Program Expedition 329. Anoxic and oxic sediment slurry enrichments using fresh sediment were used to isolate multiple fungal strains in media types that varied in organic carbon substrates and concentration. Metabolically active and dormant fungal populations were also determined from nucleic acids extracted from in situ cryopreserved South Pacific Gyre sediments. For further characterization of physical growth parameters, two isolates were chosen based on their representation of the whole South Pacific Gyre fungal community. Results from this study show that fungi have adapted to be metabolically active and key community members in South Pacific Gyre sediments and potentially within global biogeochemical cycles.
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Affiliation(s)
- Brandi Kiel Reese
- Dauphin Island Sea Lab, Dauphin Island, AL, United States
- School of Marine and Environmental Sciences, University of South Alabama, Mobile, AL, United States
- Hanse-Wissenschaftskolleg Institute for Advanced Study, Delmenhorst, Germany
| | - Morgan S. Sobol
- Institute for Biological Interfaces 5, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Life Sciences, Texas A&M University, Corpus Christi, TX, United States
| | | | - Kai-Uwe Hinrichs
- MARUM-Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
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Perez M, Angers B, Young CR, Juniper SK. Shining light on a deep-sea bacterial symbiont population structure with CRISPR. Microb Genom 2021; 7. [PMID: 34448690 PMCID: PMC8549365 DOI: 10.1099/mgen.0.000625] [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] [Indexed: 01/04/2023] Open
Abstract
Many foundation species in chemosynthesis-based ecosystems rely on environmentally acquired symbiotic bacteria for their survival. Hence, understanding the biogeographic distributions of these symbionts at regional scales is key to understanding patterns of connectivity and predicting resilience of their host populations (and thus whole communities). However, such assessments are challenging because they necessitate measuring bacterial genetic diversity at fine resolutions. For this purpose, the recently discovered clustered regularly interspaced short palindromic repeats (CRISPR) constitutes a promising new genetic marker. These DNA sequences harboured by about half of bacteria hold their viral immune memory, and as such, might allow discrimination of different lineages or strains of otherwise indistinguishable bacteria. In this study, we assessed the potential of CRISPR as a hypervariable phylogenetic marker in the context of a population genetic study of an uncultured bacterial species. We used high-throughput CRISPR-based typing along with multi-locus sequence analysis (MLSA) to characterize the regional population structure of the obligate but environmentally acquired symbiont species Candidatus Endoriftia persephone on the Juan de Fuca Ridge. Mixed symbiont populations of Ca. Endoriftia persephone were sampled across individual Ridgeia piscesae hosts from contrasting habitats in order to determine if environmental conditions rather than barriers to connectivity are more important drivers of symbiont diversity. We showed that CRISPR revealed a much higher symbiont genetic diversity than the other housekeeping genes. Several lines of evidence imply this diversity is indicative of environmental strains. Finally, we found with both CRISPR and gene markers that local symbiont populations are strongly differentiated across sites known to be isolated by deep-sea circulation patterns. This research showed the high power of CRISPR to resolve the genetic structure of uncultured bacterial populations and represents a step towards making keystone microbial species an integral part of conservation policies for upcoming mining operations on the seafloor.
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Garrido-Sanz D, Redondo-Nieto M, Martin M, Rivilla R. Comparative genomics of the Pseudomonas corrugata subgroup reveals high species diversity and allows the description of Pseudomonas ogarae sp. nov. Microb Genom 2021; 7:000593. [PMID: 34184980 PMCID: PMC8461476 DOI: 10.1099/mgen.0.000593] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/26/2021] [Indexed: 12/29/2022] Open
Abstract
Pseudomonas corrugata constitute one of the phylogenomic subgroups within the Pseudomonas fluorescens species complex and include both plant growth-promoting rhizobacteria (PGPR) and plant pathogenic bacteria. Previous studies suggest that the species diversity of this group remains largely unexplored together with frequent misclassification of strains. Using more than 1800 sequenced Pseudomonas genomes we identified 121 genomes belonging to the P. corrugata subgroup. Intergenomic distances obtained using the genome-to-genome blast distance (GBDP) algorithm and the determination of digital DNA-DNA hybridization values were further used for phylogenomic and clustering analyses, which revealed 29 putative species clusters, of which only five correspond to currently named species within the subgroup. Comparative and functional genome-scale analyses also support the species status of these clusters. The search for PGPR and plant pathogenic determinants showed that approximately half of the genomes analysed could have a pathogenic behaviour based on the presence of a pathogenicity genetic island, while all analysed genomes possess PGPR traits. Finally, this information together with the characterization of phenotypic traits, allows the reclassification proposal of Pseudomonas fluorescens F113 as Pseudomonas ogarae sp. nov., nom rev., type strain F113T (=DSM 112162T=CECT 30235T), which is substantiated by genomic, functional genomics and phenotypic differences with their closest type strains.
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Affiliation(s)
- Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
- Department of Fundamental Microbiology, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Marta Martin
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin 2, 28049 Madrid, Spain
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21
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Maguvu TE, Oladipo AO, Bezuidenhout CC. Analysis of Genome Sequences of Coagulase-Negative Staphylococci Isolates from South Africa and Nigeria Highlighted Environmentally Driven Heterogeneity. J Genomics 2021; 9:26-37. [PMID: 34025805 PMCID: PMC8133835 DOI: 10.7150/jgen.53019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 10/28/2020] [Indexed: 11/27/2022] Open
Abstract
Here, we report high-quality annotated draft genomes of eight coagulase-negative staphylococci (CoNS) isolates obtained from South Africa and Nigeria. We explored the prevalence of antibiotic resistance and virulence genes, their association with mobile genetic elements. The pan-genomic analysis highlighted the environmentally driven heterogeneity of the isolates. Isolates from Nigeria had at least one gene for cadmium resistance/tolerance, these genes were not detected in isolates from South Africa. In contrast, isolates from South Africa had a tetM gene, which was not detected among the isolates from Nigeria. The observed genomic heterogeneity correlates with anthropogenic activities in the area where the isolates were collected. Moreover, the isolates used in this study possess an open pan-genome, which could easily explain the environmentally driven heterogeneity.
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Affiliation(s)
- Tawanda Elias Maguvu
- Unit for Environmental Sciences and Management: Microbiology, North-West University, Potchefstroom, South Africa. Private Bag X6001, Potchefstroom, 2520, South Africa
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22
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van der Loo C, Bartie C, Barnard TG, Potgieter N. Detection of Free-Living Amoebae and Their Intracellular Bacteria in Borehole Water before and after a Ceramic Pot Filter Point-of-Use Intervention in Rural Communities in South Africa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:3912. [PMID: 33917870 PMCID: PMC8068299 DOI: 10.3390/ijerph18083912] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 11/21/2022]
Abstract
Free-living amoebae (FLA) are ubiquitous in nature, whereas amoeba-resistant bacteria (ARB) have evolved virulent mechanisms that allow them to resist FLA digestion mechanisms and survive inside the amoeba during hostile environmental conditions. This study assessed the prevalence of FLA and ARB species in borehole water before and after a ceramic point-of-use intervention in rural households. A total of 529 water samples were collected over a five-month period from 82 households. All water samples were subjected to amoebal enrichment, bacterial isolation on selective media, and molecular identification using 16S PCR/sequencing to determine ARB species and 18S rRNA PCR/sequencing to determine FLA species present in the water samples before and after the ceramic pot intervention. Several FLA species including Acanthamoeba spp. and Mycobacterium spp. were isolated. The ceramic pot filter removed many of these microorganisms from the borehole water. However, design flaws could have been responsible for some FLA and ARB detected in the filtered water. FLA and their associated ARB are ubiquitous in borehole water, and some of these species might be potentially harmful and a health risk to vulnerable individuals. There is a need to do more investigations into the health risk of these organisms after point-of-use treatment.
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Affiliation(s)
- Clarissa van der Loo
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, Johannesburg 2094, South Africa; (C.v.d.L.); (T.G.B.)
| | | | - Tobias George Barnard
- Water and Health Research Centre, Faculty of Health Sciences, University of Johannesburg, Johannesburg 2094, South Africa; (C.v.d.L.); (T.G.B.)
| | - Natasha Potgieter
- Environmental Health, Domestic Hygiene and Microbial Pathogens Research Group, Department of Microbiology, University of Venda, Thohoyandou 1950, South Africa
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23
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Sándor Z, Kincses I, Tállai M, Lowy DA, Melendez JR, Guananga Diaz NI, Guevara Iñiguez LE, Cuenca Nevarez G, Talledo Solórzano V, Kátai J. Effect of herbicides on soil respiration: a case study conducted at Debrecen-Látókép Plant Cultivation Experimental Station. F1000Res 2021; 9:1348. [PMID: 33728045 PMCID: PMC7919601 DOI: 10.12688/f1000research.27057.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/10/2020] [Indexed: 11/20/2022] Open
Abstract
Measuring the effect of herbicides on the natural environment is essential to secure sustainable agriculture practices. Amount of carbon dioxide released by soil microorganisms (soil respiration) is one of the most important soil health indicators, known so far. In this paper we present a comprehensive quantifying study, in which we measured the effect of 14 herbicides on soil respiration over 16 years, from 1991 to 2017, at Debrecen-Látókép Plant Cultivation Experimental Station. Investigated herbicides contained different active ingredients and were applied in various doses. It was found that 11 out of the examined 14 herbicides had a detrimental effect on soil respiration.
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Affiliation(s)
- Zsolt Sándor
- Institute of Agrochemistry and Soil Science, University of Debrecen, Debrecen, Hungary.,Research Group of Applied Plant Glycobiology, Dama Research Center limited, Kowloon, Hong Kong
| | - Ida Kincses
- Institute of Agrochemistry and Soil Science, University of Debrecen, Debrecen, Hungary
| | - Magdolna Tállai
- Institute of Agrochemistry and Soil Science, University of Debrecen, Debrecen, Hungary
| | - Daniel A Lowy
- Genesis Sustainable Future, Ltd., Sárospatak, Hungary
| | - Jesus R Melendez
- Research Group of Applied Plant Glycobiology, Dama Research Center limited, Kowloon, Hong Kong.,Facultad Educación Técnica para el Desarrollo, Universidad Católica de Santiago de Guayaquil, Guayaquil, Ecuador
| | - Nelly Ivonne Guananga Diaz
- Research Group of Applied Plant Glycobiology, Dama Research Center limited, Kowloon, Hong Kong.,Escuela Superior Politécnica de Chimborazo, Riobamba, Ecuador
| | | | | | | | - János Kátai
- Institute of Agrochemistry and Soil Science, University of Debrecen, Debrecen, Hungary
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24
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Li A, Li G, Yang J, Yang Y, Liang Y, Zhang D. Geo-distribution pattern of microbial carbon cycling genes responsive to petroleum contamination in continental horizontal oilfields. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 731:139188. [PMID: 32402908 DOI: 10.1016/j.scitotenv.2020.139188] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 05/01/2020] [Accepted: 05/01/2020] [Indexed: 06/11/2023]
Abstract
Contamination significantly affects soil microbial community structures, and the metabolisms of organic contaminants might particularly alter soil carbon cycling by shaping microbial carbon cycling genes. Although numerous studies have discussed the impacts of petroleum contamination on soil bacterial communities and relevant degrading genes, there is no work addressing how soil carbon cycling genes are affected by petroleum contamination. In this study, 77 soil samples were collected from five typical oilfields horizontally located in China to explore the influence of environmental variables and petroleum contamination on microbial carbon cycling genes. Results from Geochip suggested a geographic-determined distribution of carbon cycling genes. Although no significant correlation was observed between carbon cycling genes and soil physio-chemical properties for all soils, some relationships were identified in specific oilfield. Principle component analysis indicated that soil physio-chemical properties, rather than petroleum contamination disturbance, are the key factors determining the degree of sample dispersion, whereas environmental variables predominantly control the degree of sample aggregation. Co-occurrence ecological network analysis revealed a more complex interactions of all functional genes in petroleum-contaminated soils, and carbon cycling genes were grouped with nitrogen related genes in petroleum-contaminated communities. Soil moisture and heterogeneity were identified as the main drivers for the abundance and diversity of carbon cycling genes, particularly in petroleum-contaminated soils. These results are attributing to the fewer impacts of petroleum contamination on the diversity of carbon cycling genes than soil physio-chemical properties, and soil carbon cycling genes are mainly driven by geographic location and petroleum contamination together. Our findings provide deeper insight into the influence of petroleum contamination in soil microbial functions related to carbon cycling.
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Affiliation(s)
- Aiyang Li
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China
| | - Guanghe Li
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, People's Republic of China
| | - Juejie Yang
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yunfeng Yang
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yuting Liang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, People's Republic of China.
| | - Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, People's Republic of China; State Key Joint Lab of Environment Simulation & Pollution Control, Tsinghua University, Beijing 100084, People's Republic of China; National Engineering Laboratory for Site Remediation Technologies, Beijing 100015, People's Republic of China.
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25
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Gilbert KJ, Bittleston LS, Naive MAK, Kiszewski AE, Buenavente PAC, Lohman DJ, Pierce NE. Investigation of an Elevational Gradient Reveals Strong Differences Between Bacterial and Eukaryotic Communities Coinhabiting Nepenthes Phytotelmata. MICROBIAL ECOLOGY 2020; 80:334-349. [PMID: 32291478 PMCID: PMC7371667 DOI: 10.1007/s00248-020-01503-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/25/2020] [Indexed: 05/24/2023]
Abstract
Elevation is an important determinant of ecological community composition. It integrates several abiotic features and leads to strong, repeatable patterns of community structure, including changes in the abundance and richness of numerous taxa. However, the influence of elevational gradients on microbes is understudied relative to plants and animals. To compare the influence of elevation on multiple taxa simultaneously, we sampled phytotelm communities within a tropical pitcher plant (Nepenthes mindanaoensis) along a gradient from 400 to 1200 m a.s.l. We use a combination of metabarcoding and physical counts to assess diversity and richness of bacteria, micro-eukaryotes, and arthropods, and compare the effect of elevation on community structure to that of regulation by a number of plant factors. Patterns of community structure differed between bacteria and eukaryotes, despite their living together in the same aquatic microhabitats. Elevation influences community composition of eukaryotes to a significantly greater degree than it does bacteria. When examining pitcher characteristics, pitcher dimorphism has an effect on eukaryotes but not bacteria, while variation in pH levels strongly influences both taxa. Consistent with previous ecological studies, arthropod abundance in phytotelmata decreases with elevation, but some patterns of abundance differ between living inquilines and prey.
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Affiliation(s)
- Kadeem J Gilbert
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA.
- Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, PA, 16802, USA.
| | - Leonora S Bittleston
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 1-290, Cambridge, MA, 02139, USA
- Department of Biological Sciences, Boise State University, 1910 W University Dr, Boise, ID, 83725, USA
| | - Mark Arcebal K Naive
- Department of Biological Sciences, College of Science and Mathematics, Mindanao State University-Iligan Institute of Technology, Andres Bonifacio Ave, 9200, Iligan, Lanao del Norte, Philippines
| | - Anthony E Kiszewski
- Department of Natural and Applied Sciences, Bentley University, 175 Forest Street, Waltham, MA, 02452, USA
| | | | - David J Lohman
- Entomology Section, National Museum of Natural History, Manila, Philippines
- Biology Department, City College of New York, City University of New York, New York, NY, USA
- Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY, USA
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA
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26
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Wang C, Michalet R, Liu Z, Jiang X, Wang X, Zhang G, An L, Chen S, Xiao S. Disentangling Large- and Small-Scale Abiotic and Biotic Factors Shaping Soil Microbial Communities in an Alpine Cushion Plant System. Front Microbiol 2020; 11:925. [PMID: 32528430 PMCID: PMC7262953 DOI: 10.3389/fmicb.2020.00925] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/20/2020] [Indexed: 12/20/2022] Open
Abstract
Microorganisms play a crucial role in biogeochemical cycles and ecosystem processes, but the key factors driving microbial community structure are poorly understood, particularly in alpine environments. In this study, we aim to disentangle the relative contribution of abiotic and biotic factors shaping bacterial and fungal community structure at large and small spatial and integration scales in an alpine system dominated by a stress-tolerant cushion species Thylacospermum ceaspitosum. These effects were assessed in two mountain ranges of northwest China and for two contrasting phenotypes of the cushion species inhabiting two different microtopographic positions. The large- and small-scale abiotic effects include the site and microhabitat effects, respectively, while the large- and small-scale biotic effects include the effects of cushion presence and cushion phenotype, respectively. Soil microbial communities were characterized by Illumina Miseq sequencing. Uni- and multivariate statistics were used to test the effects of abiotic and biotic factors at both scales. Results indicated that the site effect representing the soil pH and abiotic hydrothermal conditions mainly affected bacterial community structure, whereas fungal community structure was mainly affected by biotic factors with an equal contribution of cushion presence and cushion phenotype effects. Future studies should analyze the direct factors contributing to shaping microbial community structure in particular of the cushion phenotypes.
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Affiliation(s)
- Chenyue Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
| | - Richard Michalet
- Environnements et Paléoenvironnements Océaniques et Continentaux, University of Bordeaux, Bordeaux, France
| | - Ziyang Liu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
| | - Xingpei Jiang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
| | - Xiangtai Wang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
| | - Gaosen Zhang
- Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, China.,Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou, China
| | - Lizhe An
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
| | - Shuyan Chen
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
| | - Sa Xiao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, China
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27
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Polonca S. Environment Shapes the Intra-species Diversity of Bacillus subtilis Isolates. MICROBIAL ECOLOGY 2020; 79:853-864. [PMID: 31707464 DOI: 10.1007/s00248-019-01455-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 10/23/2019] [Indexed: 06/10/2023]
Abstract
Cosmopolitan bacteria are those that are found practically everywhere in the world. One of them is Bacillus subtilis, which can travel around the world through dust storms rising from various deserts. Upon landing, bacterial survival is determined by the ability to adjust to the heterogonous environments and bacteria isolated from extremely different environments, such as desert and riverbank soil, are expected to be less related due to the environmental pressure of each region. However, little is known about the influence of soil and habitat on B. subtilis evolution. Here, we show that desert and riverbank B. subtilis strains differ in genetic relatedness and physiological traits, such as biofilm morphology and utilisation of carbon sources. Desert strains showed more diversity at the genetic level and were able to utilise more carbon sources than riverbank strains which were highly genetically conserved. Biofilm morphologies of desert and riverbank strains generally segregated and both groups formed different morphology clusters despite the astonishing diversity observed among riverbank strains. We also show that relatedness of B. subtilis strains does not decrease with distance inside the same habitat, which, together with diversity data implies that the difference in environmental selection pressures plays a fundamental role in the evolution of this species.
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Affiliation(s)
- Stefanic Polonca
- Biotechnical Faculty, University of Ljubljana, 1000, Ljubljana, Slovenia.
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28
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Li J, Gu X, Gui Y. Prokaryotic Diversity and Composition of Sediments From Prydz Bay, the Antarctic Peninsula Region, and the Ross Sea, Southern Ocean. Front Microbiol 2020; 11:783. [PMID: 32411115 PMCID: PMC7198716 DOI: 10.3389/fmicb.2020.00783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/01/2020] [Indexed: 11/13/2022] Open
Abstract
The V3–V4 hypervariable regions of the 16S ribosomal RNA gene were analyzed to assess prokaryotic diversity and community compositions within 19 surface sediment samples collected from three different regions (depth: 250–3,548 m) of Prydz Bay, the Antarctic Peninsula region, and the Ross Sea. In our results, we characterized 1,079,709 clean tag sequences representing 43,227 operational taxonomic units (OTUs, 97% similarity). The prokaryotic community distribution exhibited obvious geographical differences, and the sequences formed three distinct clusters according to the samples’ origins. In general, the biodiversity of Prydz Bay was higher than those of the Antarctic Peninsula region and the Ross Sea, and there were similar prokaryotic communities in different geographic locations. The most dominant clades in the prokaryotic communities were Proteobacteria, Bacteroidetes, Thaumarchaeota, Oxyphotobacteria, Deinococcus-Thermus, Firmicutes, Acidobacteria, Fusobacteria, and Planctomycetes, but unique prokaryotic community compositions were found in each of the sampling regions. Our results also demonstrated that the prokaryotic diversity and community distribution were mainly influenced by geographical and physicochemical factors, such as Zn, V, Na, K, water depth, and especially geographical distance (longitude variation of sample location) and Ba ion content. Moreover, geochemical factors such as nutrient contents (TC, P, and Ca) also played important roles in prokaryotic diversity and community distribution. This represents the first report that Ba ion content has an obvious effect on prokaryotic diversity and community distribution in Southern Ocean sediments.
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Affiliation(s)
- Jiang Li
- Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Ministry of Natural Resources (MNR) Key Lab for Science & Technology of Marine Ecosystems, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Xiaoqian Gu
- Marine Bioresource and Environment Research Center, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China.,Ministry of Natural Resources (MNR) Key Lab for Science & Technology of Marine Ecosystems, First Institute of Oceanography, Ministry of Natural Resources, Qingdao, China
| | - Yuanyuan Gui
- College of Environmental Science and Engineering Qingdao University, Qingdao, China
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29
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Bull AT, Goodfellow M. Dark, rare and inspirational microbial matter in the extremobiosphere: 16 000 m of bioprospecting campaigns. MICROBIOLOGY-SGM 2020; 165:1252-1264. [PMID: 31184575 DOI: 10.1099/mic.0.000822] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The rationale of our bioprospecting campaigns is that the extremobiosphere, particularly the deep sea and hyper-arid deserts, harbours undiscovered biodiversity that is likely to express novel chemistry and biocatalysts thereby providing opportunities for therapeutic drug and industrial process development. We have focused on actinobacteria because of their frequent role as keystone species in soil ecosystems and their unrivalled track record as a source of bioactive compounds. Population numbers and diversity of actinobacteria in the extremobiosphere are traditionally considered to be low, although they often comprise the dominant bacterial biota. Recent metagenomic evaluation of 'the uncultured microbial majority' has now revealed enormous taxonomic diversity among 'dark' and 'rare' actinobacteria in samples as diverse as sediments from the depths of the Mariana Trench and soils from the heights of the Central Andes. The application of innovative culture and screening options that emphasize rigorous dereplication at each stage of the analysis, and strain prioritization to identify 'gifted' organisms, have been deployed to detect and characterize bioactive hit compounds and sought-after catalysts from this hitherto untapped resource. The rewards include first-in-a-class chemical entities with novel modes of action, as well as a growing microbial seed bank that represents a potentially enormous source of biotechnological and therapeutic innovation.
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Affiliation(s)
- Alan T Bull
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Ridley Building 2, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
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30
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Draft Genome Sequence of Pseudomonas sp. Strain LD120, Isolated from the Marine Alga Saccharina latissima. Microbiol Resour Announc 2020; 9:9/8/e01305-19. [PMID: 32079630 PMCID: PMC7033267 DOI: 10.1128/mra.01305-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report the draft genome sequence of Pseudomonas sp. strain LD120, which was isolated from a brown macroalga in the Baltic Sea. The genome of this marine Pseudomonas protegens subgroup bacterium harbors biosynthetic gene clusters for toxic metabolites typically produced by members of this Pseudomonas subgroup, including 2,4-diacetylphloroglucinol, pyoluteorin, and rhizoxin analogs. We report the draft genome sequence of Pseudomonas sp. strain LD120, which was isolated from a brown macroalga in the Baltic Sea. The genome of this marine Pseudomonas protegens subgroup bacterium harbors biosynthetic gene clusters for toxic metabolites typically produced by members of this Pseudomonas subgroup, including 2,4-diacetylphloroglucinol, pyoluteorin, and rhizoxin analogs.
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31
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Ung L, Bispo PJM, Bryan NC, Andre C, Chodosh J, Gilmore MS. The Best of All Worlds: Streptococcus pneumoniae Conjunctivitis through the Lens of Community Ecology and Microbial Biogeography. Microorganisms 2019; 8:microorganisms8010046. [PMID: 31881682 PMCID: PMC7022640 DOI: 10.3390/microorganisms8010046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/16/2019] [Accepted: 12/21/2019] [Indexed: 12/16/2022] Open
Abstract
The study of the forces which govern the geographical distributions of life is known as biogeography, a subject which has fascinated zoologists, botanists and ecologists for centuries. Advances in our understanding of community ecology and biogeography—supported by rapid improvements in next generation sequencing technology—have now made it possible to identify and explain where and why life exists as it does, including within the microbial world. In this review, we highlight how a unified model of microbial biogeography, one which incorporates the classic ecological principles of selection, diversification, dispersion and ecological drift, can be used to explain community dynamics in the settings of both health and disease. These concepts operate on a multiplicity of temporal and spatial scales, and together form a powerful lens through which to study microbial population structures even at the finest anatomical resolutions. When applied specifically to curious strains of conjunctivitis-causing, nonencapsulated Streptococcus pneumoniae, we show how this conceptual framework can be used to explain the possible evolutionary and disease-causing mechanisms which allowed these lineages to colonize and invade a separate biogeography. An intimate knowledge of this radical bifurcation in phylogeny, still the only known niche subspecialization for S. pneumoniae to date, is critical to understanding the pathogenesis of ocular surface infections, nature of host-pathogen interactions, and developing strategies to curb disease transmission.
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Affiliation(s)
- Lawson Ung
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA; (L.U.); (P.J.M.B.); (C.A.); (J.C.)
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA;
| | - Paulo J. M. Bispo
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA; (L.U.); (P.J.M.B.); (C.A.); (J.C.)
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA;
| | - Noelle C. Bryan
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA;
- Massachusetts Institute of Technology, Department of Earth, Atmospheric and Planetary Sciences, Cambridge, MA 02139, USA
| | - Camille Andre
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA; (L.U.); (P.J.M.B.); (C.A.); (J.C.)
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA;
| | - James Chodosh
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA; (L.U.); (P.J.M.B.); (C.A.); (J.C.)
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA;
| | - Michael S. Gilmore
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA; (L.U.); (P.J.M.B.); (C.A.); (J.C.)
- Infectious Disease Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA 02114, USA;
- Correspondence: ; Tel.: +1-617-523-7900
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32
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Xing R, Gao Q, Zhang F, Wang J, Chen S. Large-scale distribution of bacterial communities in the Qaidam Basin of the Qinghai-Tibet Plateau. Microbiologyopen 2019; 8:e909. [PMID: 31452349 PMCID: PMC6813490 DOI: 10.1002/mbo3.909] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/10/2019] [Accepted: 06/30/2019] [Indexed: 11/23/2022] Open
Abstract
Many studies have investigated patterns of soil microbial communities over large spatial scales. However, these studies mainly focused on a few sites. Here, we studied the near‐surface (0–30 cm) soil microbial communities of 35 soil samples collected from most of the areas of the Qaidam Basin, which is the largest basin on the Qinghai–Tibet Plateau. A total of 32 phyla and 838 genera were detected from all the samples, in which Actinobacteria, Proteobacteria, Bacteroidetes, and Acidobacteria were the most dominant and cosmopolitan phyla. The most abundant phyla (relative abundance > 5%) detected in all 35 soil samples were also the most dominant, which could be explained by their great dispersal ability. The microbial community structures correlated strongly with variations in pH and Mg2+ and were distinct between the high Mg2+ content (>20 g/kg) samples and other samples (Acidobacteria, Actinobacteria, and Chloroflexi were significantly less abundant in the high Mg2+ content group, but the abundance of Firmicutes was significantly greater). Finally, the microbial spatial pattern was influenced by both the local environment and spatial distance, but environmental factors were the primary drivers of microbial spatial patterns in the Qaidam Basin.
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Affiliation(s)
- Rui Xing
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
- Qinghai Provincial Key Laboratory of Crop Molecular BreedingXiningQinghaiChina
| | - Qing‐bo Gao
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
| | - Fa‐qi Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
| | - Jiu‐li Wang
- Qinghai Nationalities UniversityXiningQinghaiChina
| | - Shi‐long Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau BiologyChinese Academy of SciencesXiningQinghaiChina
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33
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Zhang X, Liu X, Li L, Wei G, Zhang D, Liang Y, Miao B. Phylogeny, Divergent Evolution, and Speciation of Sulfur-Oxidizing Acidithiobacillus Populations. BMC Genomics 2019; 20:438. [PMID: 31146680 PMCID: PMC6543593 DOI: 10.1186/s12864-019-5827-6] [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] [Received: 04/23/2019] [Accepted: 05/23/2019] [Indexed: 01/18/2023] Open
Abstract
Background Habitats colonized by acidophiles as an ideal physical barrier may induce genetic exchange of microbial members within the common communities, but little is known about how species in extremely acidic environments diverge and evolve. Results Using the acidophilic sulfur-oxidizer Acidithiobacillus as a case study, taxonomic reclassifications of many isolates provides novel insights into their phylogenetic lineage. Whole-genome-based comparisons were attempted to investigate the intra- and inter-species divergence. Recent studies clarified that functional and structural specificities of bacterial strains might provide opportunities for adaptive evolution responding to local environmental conditions. Acidophilic microorganisms play a key role in the acidification of natural waters and thus the formation of extremely acidic environments, and the feedbacks of the latter might confer the distinct evolutionary patterns of Acidithiobacillus spp. Varied horizontal gene transfer events occurred in different bacterial strains, probably resulting in the expansion of Acidithiobacillus genomes. Gene loss as another evolutionary force might cause the adaptive phenotypic diversity. A conceptual model for potential community-dependent evolutionary adaptation was thus proposed to illustrate the observed genome differentiation. Conclusions Collectively, the findings shed light on the phylogeny and divergent evolution of Acidithiobacillus strains, and provided a useful reference for evolutionary studies of other extremophiles. Electronic supplementary material The online version of this article (10.1186/s12864-019-5827-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xian Zhang
- Department of Occupational and Environmental Health, Xiangya School of Public Health, Central South University, Changsha, China.
| | - Xueduan Liu
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
| | - Guanyun Wei
- School of Life Sciences, Nantong University, Nantong, China
| | - Danli Zhang
- Department of Biology, Taiyuan Normal University, Taiyuan, China
| | - Yili Liang
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Bo Miao
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China.,Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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34
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Zhang FG, Bell T, Zhang QG. Experimental Testing of Dispersal Limitation in Soil Bacterial Communities with a Propagule Addition Approach. MICROBIAL ECOLOGY 2019; 77:905-912. [PMID: 30417222 DOI: 10.1007/s00248-018-1284-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 10/29/2018] [Indexed: 06/09/2023]
Abstract
The role of dispersal in the assembly of microbial communities remains contentious. This study tested the importance of dispersal limitation for the structuring of local soil bacterial communities using an experimental approach of propagule addition. Microbes extracted from soil pooled from samples collected at 20 localities across ~ 400 km in a temperate steppe were added to microcosms of local soils at three sites; the microcosms were then incubated in situ for 3 months. We then assessed the composition and diversity of bacterial taxa in the soils using 16S rRNA gene amplicon sequencing. The addition of the regional microbial pool did not cause significant changes in the overall composition or diversity of the total bacterial community, although a very small number of individual taxa may have been affected by the addition treatment. Our results suggest a negligible role of dispersal limitation in structuring soil bacterial communities in our study area.
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Affiliation(s)
- Fen-Guo Zhang
- College of Life Sciences, Shanxi Normal University, Linfen, 041004, Shanxi, China
| | - Thomas Bell
- Department of Life Sciences, Imperial College London, Ascot, Berkshire, SL5 7PY, UK
| | - Quan-Guo Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and MOE Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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35
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Oni FE, Geudens N, Omoboye OO, Bertier L, Hua HGK, Adiobo A, Sinnaeve D, Martins JC, Höfte M. Fluorescent Pseudomonas and cyclic lipopeptide diversity in the rhizosphere of cocoyam (Xanthosoma sagittifolium). Environ Microbiol 2019; 21:1019-1034. [PMID: 30623562 DOI: 10.1111/1462-2920.14520] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 12/21/2022]
Abstract
Cocoyam (Xanthosoma sagittifolium (L.)), an important tuber crop in the tropics, is severely affected by the cocoyam root rot disease (CRRD) caused by Pythium myriotylum. The white cocoyam genotype is very susceptible while the red cocoyam has some field tolerance to CRRD. Fluorescent Pseudomonas isolates obtained from the rhizosphere of healthy red and white cocoyams from three different fields in Cameroon were taxonomically characterized. The cocoyam rhizosphere was enriched with P. fluorescens complex and P. putida isolates independent of the plant genotype. LC-MS and NMR analyses revealed that 50% of the Pseudomonas isolates produced cyclic lipopeptides (CLPs) including entolysin, lokisin, WLIP, putisolvin and xantholysin together with eight novel CLPs. In general, CLP types were linked to specific taxonomic groups within the fluorescent pseudomonads. Representative CLP-producing bacteria showed effective control against CRRD while purified CLPs caused hyphal branching or hyphal leakage in P. myriotylum. The structure of cocoyamide A, a CLP which is predominantly produced by P. koreensis group isolates within the P. fluorescens complex is described. Compared with the white cocoyam, the red cocoyam rhizosphere appeared to support a more diverse CLP spectrum. It remains to be investigated whether this contributes to the field tolerance displayed by the red cocoyam.
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Affiliation(s)
- Feyisara Eyiwumi Oni
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Niels Geudens
- NMR and Structural Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000, Ghent, Belgium
| | - Olumide Owolabi Omoboye
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Lien Bertier
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Hoang Gia Khuong Hua
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
| | - Amayana Adiobo
- Jay PJ Biotechnology Laboratory, Institute for Agricultural Research for Development (IRAD), Ekona, P.M.B 25, Buea, Cameroon
| | - Davy Sinnaeve
- NMR and Structural Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000, Ghent, Belgium
| | - José C Martins
- NMR and Structural Analysis Unit, Department of Organic and Macromolecular Chemistry, Faculty of Science, Ghent University, Krijgslaan 281, B-9000, Ghent, Belgium
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium
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36
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Microbiota dispersion in the Uyuni salt flat (Bolivia) as determined by community structure analyses. Int Microbiol 2019; 22:325-336. [DOI: 10.1007/s10123-018-00052-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/13/2018] [Accepted: 12/10/2018] [Indexed: 10/27/2022]
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37
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Wei H, Peng C, Yang B, Song H, Li Q, Jiang L, Wei G, Wang K, Wang H, Liu S, Liu X, Chen D, Li Y, Wang M. Contrasting Soil Bacterial Community, Diversity, and Function in Two Forests in China. Front Microbiol 2018; 9:1693. [PMID: 30108560 PMCID: PMC6080587 DOI: 10.3389/fmicb.2018.01693] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 07/06/2018] [Indexed: 12/03/2022] Open
Abstract
Bacteria are the highest abundant microorganisms in the soil. To investigate bacteria community structures, diversity, and functions, contrasting them in four different seasons all the year round with/within two different forest type soils of China. We analyzed soil bacterial community based on 16S rRNA gene sequencing via Illumina HiSeq platform at a temperate deciduous broad-leaved forest (Baotianman, BTM) and a tropical rainforest (Jianfengling, JFL). We obtained 51,137 operational taxonomic units (OTUs) and classified them into 44 phyla and 556 known genera, 18.2% of which had a relative abundance >1%. The composition in each phylum was similar between the two forest sites. Proteobacteria and Acidobacteria were the most abundant phyla in the soil samples between the two forest sites. The Shannon index did not significantly differ among the four seasons at BTM or JFL and was higher at BTM than JFL in each season. The bacteria community at both BTM and JFL showed two significant (P < 0.05) predicted functions related to carbon cycle (anoxygenic photoautotrophy sulfur oxidizing and anoxygenic photoautotrophy) and three significant (P < 0.05) predicted functions related to nitrogen cycle (nitrous denitrificaton, nitrite denitrification, and nitrous oxide denitrification). We provide the basis on how changes in bacterial community composition and diversity leading to differences in carbon and nitrogen cycles at the two forests.
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Affiliation(s)
- Hua Wei
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China.,Medical College, Baoji Vocational Technology College, Baoji, China
| | - Changhui Peng
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China.,Départment des Sciences Biologiques, Institut des Sciences de l'Environnement, Université du Québec à Montréal, Montreal, QC, Canada
| | - Bin Yang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Hanxiong Song
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Quan Li
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Lin Jiang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Gang Wei
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Kefeng Wang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Hui Wang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China
| | - Shirong Liu
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| | - Xiaojing Liu
- Baotianman Natural Reserve Administration, Neixiang, China
| | - Dexiang Chen
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Yide Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Meng Wang
- Center for Ecological Forecasting and Global Change, College of Forestry, Northwest A&F University, Yangling, China.,State Environmental Protection Key Laboratory of Wetland Ecology and Vegetation Restoration, Institute for Peat and Mire Research, Northeast Normal University, Changchun, China
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38
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Microbial Diversity: The Gap between the Estimated and the Known. DIVERSITY-BASEL 2018. [DOI: 10.3390/d10020046] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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39
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Han D, Wang N, Sun X, Hu Y, Feng F. Biogeographical distribution of bacterial communities in Changbai Mountain, Northeast China. Microbiologyopen 2018; 7:e00529. [PMID: 29446229 PMCID: PMC5911996 DOI: 10.1002/mbo3.529] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/11/2017] [Accepted: 07/18/2017] [Indexed: 11/10/2022] Open
Abstract
The broad-leaved and Korean pine mixed forest in Changbai Mountain, China is an important component of boreal forest; the area is sensitive to global climate change. To understand spatial distribution patterns of soil bacterial community along elevation, we analyzed the soil bacterial community diversity and composition along an elevational gradient of 699-1177 m in a primitive Korean pine forest in Changbai Mountain using the high-throughput sequencing. In total, 149,519 optimized sequences were obtained. Bacterial Shannon index increased along elevation from 699 m to 937 m and started to decrease at the elevation of 1,044 m, showing a humpback curve along elevation. Evenness (ACE index) and richness (Chao index) of the soil bacterial community both decreased with elevation (the highest values of 770 and 762 at 699 m and the lowest values of 548 and 539 at 1,177 m, respectively), all the indices are significantly different between elevations. Bacterial composition at phylum and genus levels had some differences between elevations, but the dominant bacterial populations were generally consistent. Beta-diversity analysis showed a distance-decay pattern of bacterial community similarity at different samples. Soil physical and chemical properties explained 70.78% of the variation in bacterial community structure (soil pH explained 19.95%), and elevational distance only explained 8.42%. In conclusion, the contemporary environmental disturbances are the critical factors in maintaining the bacterial spatial distribution compared with historical contingencies.
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Affiliation(s)
- Dongxue Han
- Northeast Forestry University, Harbin, China.,Key Lab of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Ning Wang
- Northeast Forestry University, Harbin, China
| | - Xue Sun
- Northeast Forestry University, Harbin, China
| | - Yanbo Hu
- Northeast Forestry University, Harbin, China
| | - Fujuan Feng
- Northeast Forestry University, Harbin, China
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40
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Shi Y, Li Y, Xiang X, Sun R, Yang T, He D, Zhang K, Ni Y, Zhu YG, Adams JM, Chu H. Spatial scale affects the relative role of stochasticity versus determinism in soil bacterial communities in wheat fields across the North China Plain. MICROBIOME 2018; 6:27. [PMID: 29402331 PMCID: PMC5799910 DOI: 10.1186/s40168-018-0409-4] [Citation(s) in RCA: 186] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/19/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND The relative importance of stochasticity versus determinism in soil bacterial communities is unclear, as are the possible influences that alter the balance between these. Here, we investigated the influence of spatial scale on the relative role of stochasticity and determinism in agricultural monocultures consisting only of wheat, thereby minimizing the influence of differences in plant species cover and in cultivation/disturbance regime, extending across a wide range of soils and climates of the North China Plain (NCP). We sampled 243 sites across 1092 km and sequenced the 16S rRNA bacterial gene using MiSeq. We hypothesized that determinism would play a relatively stronger role at the broadest scales, due to the strong influence of climate and soil differences in selecting many distinct OTUs of bacteria adapted to the different environments. In order to test the more general applicability of the hypothesis, we also compared with a natural ecosystem on the Tibetan Plateau. RESULTS Our results revealed that the relative importance of stochasticity vs. determinism did vary with spatial scale, in the direction predicted. On the North China Plain, stochasticity played a dominant role from 150 to 900 km (separation between pairs of sites) and determinism dominated at more than 900 km (broad scale). On the Tibetan Plateau, determinism played a dominant role from 130 to 1200 km and stochasticity dominated at less than 130 km. Among the identifiable deterministic factors, soil pH showed the strongest influence on soil bacterial community structure and diversity across the North China Plain. Together, 23.9% of variation in soil microbial community composition could be explained, with environmental factors accounting for 19.7% and spatial parameters 4.1%. CONCLUSIONS Our findings revealed that (1) stochastic processes are relatively more important on the North China Plain, while deterministic processes are more important on the Tibetan Plateau; (2) soil pH was the major factor in shaping soil bacterial community structure of the North China Plain; and (3) most variation in soil microbial community composition could not be explained with existing environmental and spatial factors. Further studies are needed to dissect the influence of stochastic factors (e.g., mutations or extinctions) on soil microbial community distribution, which might make it easier to predictably manipulate the microbial community to produce better yield and soil sustainability outcomes.
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Affiliation(s)
- Yu Shi
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Yuntao Li
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Xingjia Xiang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Ruibo Sun
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Dan He
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Kaoping Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Yingying Ni
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021 China
| | - Jonathan M. Adams
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK46 0AL UK
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 71 East Beijing Road, Nanjing, 210008 China
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41
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Choudoir MJ, Barberán A, Menninger HL, Dunn RR, Fierer N. Variation in range size and dispersal capabilities of microbial taxa. Ecology 2018; 99:322-334. [PMID: 29160898 DOI: 10.1002/ecy.2094] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 10/31/2017] [Accepted: 11/08/2017] [Indexed: 01/25/2023]
Abstract
Geographic range size can span orders of magnitude for plant and animal species, with the study of why range sizes vary having preoccupied biogeographers for decades. In contrast, there have been few comparable studies of how range size varies across microbial taxa and what traits may be associated with this variation. We determined the range sizes of 74,134 bacterial and archaeal taxa found in settled dust collected from 1,065 locations across the United States. We found that most microorganisms have small ranges and few have large ranges, a pattern similar to the range size distributions commonly observed for macrobes. However, contrary to expectations, those microbial taxa that were locally abundant did not necessarily have larger range sizes. The observed differences in microbial range sizes were generally predictable from taxonomic identity, phenotypic traits, genomic attributes, and habitat preferences, findings that provide insight into the factors shaping patterns of microbial biogeography.
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Affiliation(s)
- Mallory J Choudoir
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, 80309, USA
| | - Albert Barberán
- Department of Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Holly L Menninger
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, 27695, USA
| | - Rob R Dunn
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, 27695, USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, 80309, USA.,Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA
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42
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Chase AB, Martiny JBH. The importance of resolving biogeographic patterns of microbial microdiversity. MICROBIOLOGY AUSTRALIA 2018. [DOI: 10.1071/ma18003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
For centuries, ecologists have used biogeographic patterns to test the processes governing the assembly and maintenance of plant and animal communities. Similarly, evolutionary biologists have used historical biogeography (e.g. phylogeography) to understand the importance of geological events as barriers to dispersal that shape species distributions. As the field of microbial biogeography initially developed, the utilisation of highly conserved marker genes, such as the 16S ribosomal RNA gene, stimulated investigations into the biogeographic patterns of the microbial community as a whole. Here, we propose that we should now consider the biogeographic patterns of microdiversity, the fine-scale genetic diversity observed within a traditional ribosomal-based operational taxonomic unit.
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43
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Flynn TM, Koval JC, Greenwald SM, Owens SM, Kemner KM, Antonopoulos DA. Parallelized, Aerobic, Single Carbon-Source Enrichments from Different Natural Environments Contain Divergent Microbial Communities. Front Microbiol 2017; 8:2321. [PMID: 29234312 PMCID: PMC5712364 DOI: 10.3389/fmicb.2017.02321] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 11/10/2017] [Indexed: 12/31/2022] Open
Abstract
Microbial communities that inhabit environments such as soil can contain thousands of distinct taxa, yet little is known about how this diversity is maintained in response to environmental perturbations such as changes in the availability of carbon. By utilizing aerobic substrate arrays to examine the effect of carbon amendment on microbial communities taken from six distinct environments (soil from a temperate prairie and forest, tropical forest soil, subalpine forest soil, and surface water and soil from a palustrine emergent wetland), we examined how carbon amendment and inoculum source shape the composition of the community in each enrichment. Dilute subsamples from each environment were used to inoculate 96-well microtiter plates containing triplicate wells amended with one of 31 carbon sources from six different classes of organic compounds (phenols, polymers, carbohydrates, carboxylic acids, amines, amino acids). After incubating each well aerobically in the dark for 72 h, we analyzed the composition of the microbial communities on the substrate arrays as well as the initial inocula by sequencing 16S rRNA gene amplicons using the Illumina MiSeq platform. Comparisons of alpha and beta diversity in these systems showed that, while the composition of the communities that grow to inhabit the wells in each substrate array diverges sharply from that of the original community in the inoculum, these enrichment communities are still strongly affected by the inoculum source. We found most enrichments were dominated by one or several OTUs most closely related to aerobes or facultative anaerobes from the Proteobacteria (e.g., Pseudomonas, Burkholderia, and Ralstonia) or Bacteroidetes (e.g., Chryseobacterium). Comparisons within each substrate array based on the class of carbon source further show that the communities inhabiting wells amended with a carbohydrate differ significantly from those enriched with a phenolic compound. Selection therefore seems to play a role in shaping the communities in the substrate arrays, although some stochasticity is also seen whereby several replicate wells within a single substrate array display strongly divergent community compositions. Overall, the use of highly parallel substrate arrays offers a promising path forward to study the response of microbial communities to perturbations in a changing environment.
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Affiliation(s)
- Theodore M Flynn
- Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
| | - Jason C Koval
- Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
| | | | - Sarah M Owens
- Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
| | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Argonne, IL, United States
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44
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Aiyar P, Schaeme D, García-Altares M, Carrasco Flores D, Dathe H, Hertweck C, Sasso S, Mittag M. Antagonistic bacteria disrupt calcium homeostasis and immobilize algal cells. Nat Commun 2017; 8:1756. [PMID: 29170415 PMCID: PMC5701020 DOI: 10.1038/s41467-017-01547-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 09/27/2017] [Indexed: 11/09/2022] Open
Abstract
Photosynthetic unicellular organisms, known as microalgae, are key contributors to carbon fixation on Earth. Their biotic interactions with other microbes shape aquatic microbial communities and influence the global photosynthetic capacity. So far, limited information is available on molecular factors that govern these interactions. We show that the bacterium Pseudomonas protegens strongly inhibits the growth and alters the morphology of the biflagellated green alga Chlamydomonas reinhardtii. This antagonistic effect is decreased in a bacterial mutant lacking orfamides, demonstrating that these secreted cyclic lipopeptides play an important role in the algal-bacterial interaction. Using an aequorin Ca2+-reporter assay, we show that orfamide A triggers an increase in cytosolic Ca2+ in C. reinhardtii and causes deflagellation of algal cells. These effects of orfamide A, which are specific to the algal class of Chlorophyceae and appear to target a Ca2+ channel in the plasma membrane, represent a novel biological activity for cyclic lipopeptides.
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Affiliation(s)
- Prasad Aiyar
- Institute of General Botany and Plant Physiology, Friedrich Schiller University, Am Planetarium 1, 07743, Jena, Germany
| | - Daniel Schaeme
- Institute of General Botany and Plant Physiology, Friedrich Schiller University, Am Planetarium 1, 07743, Jena, Germany
| | - María García-Altares
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11 a, 07745, Jena, Germany
| | - David Carrasco Flores
- Institute of General Botany and Plant Physiology, Friedrich Schiller University, Am Planetarium 1, 07743, Jena, Germany
| | - Hannes Dathe
- Institute of General Botany and Plant Physiology, Friedrich Schiller University, Am Planetarium 1, 07743, Jena, Germany
| | - Christian Hertweck
- Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11 a, 07745, Jena, Germany
| | - Severin Sasso
- Institute of General Botany and Plant Physiology, Friedrich Schiller University, Am Planetarium 1, 07743, Jena, Germany.
| | - Maria Mittag
- Institute of General Botany and Plant Physiology, Friedrich Schiller University, Am Planetarium 1, 07743, Jena, Germany.
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45
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Lopes LD, Davis EW, Pereira E Silva MDC, Weisberg AJ, Bresciani L, Chang JH, Loper JE, Andreote FD. Tropical soils are a reservoir for fluorescent Pseudomonas spp. biodiversity. Environ Microbiol 2017; 20:62-74. [PMID: 29027341 DOI: 10.1111/1462-2920.13957] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 10/07/2017] [Accepted: 10/08/2017] [Indexed: 11/30/2022]
Abstract
Fluorescent Pseudomonas spp. are widely studied for their beneficial activities to plants. To explore the genetic diversity of Pseudomonas spp. in tropical regions, we collected 76 isolates from a Brazilian soil. Genomes were sequenced and compared to known strains, mostly collected from temperate regions. Phylogenetic analyses classified the isolates in the P. fluorescens (57) and P. putida (19) groups. Among the isolates in the P. fluorescens group, most (37) were classified in the P. koreensis subgroup and two in the P. jessenii subgroup. The remaining 18 isolates fell into two phylogenetic subclades distinct from currently recognized P. fluorescens subgroups, and probably represent new subgroups. Consistent with their phylogenetic distance from described subgroups, the genome sequences of strains in these subclades are asyntenous to the genome sequences of members of their neighbour subgroups. The tropical isolates have several functional genes also present in known fluorescent Pseudomonas spp. strains. However, members of the new subclades share exclusive genes not detected in other subgroups, pointing to the potential for novel functions. Additionally, we identified 12 potential new species among the 76 isolates from the tropical soil. The unexplored diversity found in the tropical soil is possibly related to biogeographical patterns.
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Affiliation(s)
- Lucas Dantas Lopes
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil.,Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Edward W Davis
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
| | - Michele de C Pereira E Silva
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Alexandra J Weisberg
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Luana Bresciani
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
| | - Jeff H Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
| | - Joyce E Loper
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA.,Molecular and Cellular Biology Program, Oregon State University, Corvallis, OR 97331, USA
| | - Fernando D Andreote
- Department of Soil Science, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba, SP, Brazil
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46
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Wang M, Li E, Liu C, Jousset A, Salles JF. Functionality of Root-Associated Bacteria along a Salt Marsh Primary Succession. Front Microbiol 2017; 8:2102. [PMID: 29163397 PMCID: PMC5670159 DOI: 10.3389/fmicb.2017.02102] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 10/13/2017] [Indexed: 01/23/2023] Open
Abstract
Plant-associated bacteria are known for their high functional trait diversity, from which many are likely to play a role in primary and secondary succession, facilitating plant establishment in suboptimal soils conditions. Here we used an undisturbed salt marsh chronosequence that represents over 100 years of soil development to assess how the functional traits of plant associated bacteria respond to soil type, plant species and plant compartment. We isolated and characterized 808 bacterial colonies from the rhizosphere soil and root endosphere of two salt marsh plants, Limonium vulgare and Artemisia maritima, along the chronosequence. From these, a set of 59 strains (with unique BOX-PCR patterns, 16S rRNA sequence and unique to one of the treatments) were further screened for their plant growth promoting traits (siderophore production, IAA production, exoprotease production and biofilm formation), traits associated with bacterial fitness (antibiotic and abiotic stress resistance - pH, osmotic and oxidative stress, and salinity) and metabolic potential. An overall view of functional diversity (multivariate analysis) indicated that the distributional pattern of bacterial functional traits was driven by soil type. Samples from the late succession (Stage 105 year) showed the most restricted distribution, harboring strains with relatively low functionalities, whereas the isolates from intermediate stage (35 year) showed a broad functional profiles. However, strains with high trait performance were largely from stage 65 year. Grouping the traits according to category revealed that the functionality of plant endophytes did not vary along the succession, thus being driven by plant rather than soil type. In opposition, the functionality of rhizosphere isolates responded strongly to variations in soil type as observed for antibiotic resistance (P = 0.014). Specifically, certain Pseudomonas sp. and Serratia sp. strains revealed high resistance against abiotic stress and antibiotics and produce more siderophores, confirming the high plant-growth promoting activity of these two genera. Overall, this study contributes to a better understanding of the functional diversity and adaptation of the microbiome at typical salt marsh plant species across soil types. Specifically, soil type was influential only in the rhizosphere but not on the endosphere, indicating a strong plant-driven effect on the functionality of endophytes.
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Affiliation(s)
- Miao Wang
- Research Group of Microbial Community Ecology, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Erqin Li
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, Netherlands
| | - Chen Liu
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Utrecht, Netherlands
| | | | - Joana F. Salles
- Research Group of Microbial Community Ecology, Genomics Research in Ecology and Evolution in Nature, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
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47
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Tian J, He N, Hale L, Niu S, Yu G, Liu Y, Blagodatskaya E, Kuzyakov Y, Gao Q, Zhou J. Soil organic matter availability and climate drive latitudinal patterns in bacterial diversity from tropical to cold temperate forests. Funct Ecol 2017. [DOI: 10.1111/1365-2435.12952] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jing Tian
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Nianpeng He
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Lauren Hale
- Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental SciencesInstitute for Environmental GenomicsUniversity of Oklahoma Norman OK USA
| | - Shuli Niu
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Guirui Yu
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Yuan Liu
- Key Laboratory of Ecosystem Network Observation and ModelingInstitute of Geographic Sciences and Natural Resources ResearchChinese Academy of Sciences (CAS) Beijing China
| | - Evgenia Blagodatskaya
- Institute of Physicochemical and Biological Problems in Soil Science Pushchino Russia
- Department of Agricultural Soil ScienceUniversity of Göttingen Göttingen Germany
| | - Yakov Kuzyakov
- Department of Agricultural Soil ScienceUniversity of Göttingen Göttingen Germany
- Agro‐Technology InstituteRUDN University Moscow Russia
| | - Qun Gao
- Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental SciencesInstitute for Environmental GenomicsUniversity of Oklahoma Norman OK USA
- State Key Joint Laboratory of Environment Simulation and Pollution ControlSchool of EnvironmentTsinghua University Beijing China
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental SciencesInstitute for Environmental GenomicsUniversity of Oklahoma Norman OK USA
- State Key Joint Laboratory of Environment Simulation and Pollution ControlSchool of EnvironmentTsinghua University Beijing China
- Earth and Environmental SciencesLawrence Berkeley National Laboratory Berkeley CA USA
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48
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Tecon R, Or D. Biophysical processes supporting the diversity of microbial life in soil. FEMS Microbiol Rev 2017; 41:599-623. [PMID: 28961933 PMCID: PMC5812502 DOI: 10.1093/femsre/fux039] [Citation(s) in RCA: 136] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 07/10/2017] [Indexed: 12/13/2022] Open
Abstract
Soil, the living terrestrial skin of the Earth, plays a central role in supporting life and is home to an unimaginable diversity of microorganisms. This review explores key drivers for microbial life in soils under different climates and land-use practices at scales ranging from soil pores to landscapes. We delineate special features of soil as a microbial habitat (focusing on bacteria) and the consequences for microbial communities. This review covers recent modeling advances that link soil physical processes with microbial life (termed biophysical processes). Readers are introduced to concepts governing water organization in soil pores and associated transport properties and microbial dispersion ranges often determined by the spatial organization of a highly dynamic soil aqueous phase. The narrow hydrological windows of wetting and aqueous phase connectedness are crucial for resource distribution and longer range transport of microorganisms. Feedbacks between microbial activity and their immediate environment are responsible for emergence and stabilization of soil structure-the scaffolding for soil ecological functioning. We synthesize insights from historical and contemporary studies to provide an outlook for the challenges and opportunities for developing a quantitative ecological framework to delineate and predict the microbial component of soil functioning.
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Affiliation(s)
- Robin Tecon
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
| | - Dani Or
- Soil and Terrestrial Environmental Physics, Department of Environmental Systems Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
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49
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50
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Hall JPJ, Williams D, Paterson S, Harrison E, Brockhurst MA. Positive selection inhibits gene mobilisation and transfer in soil bacterial communities. Nat Ecol Evol 2017; 1:1348-1353. [PMID: 28890938 PMCID: PMC5584672 DOI: 10.1038/s41559-017-0250-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- James P J Hall
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK. .,Department of Biology, University of York, York, YO10 5DD, UK.
| | - David Williams
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, L69 7ZB, UK
| | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, L69 7ZB, UK
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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