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Cantoran A, Maillard F, Baldrian P, Kennedy PG. Defining a core microbial necrobiome associated with decomposing fungal necromass. FEMS Microbiol Ecol 2023; 99:fiad098. [PMID: 37656873 DOI: 10.1093/femsec/fiad098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 09/03/2023] Open
Abstract
Despite growing interest in fungal necromass decomposition due to its importance in soil carbon retention, whether a consistent group of microorganisms is associated with decomposing necromass remains unresolved. Here, we synthesize knowledge on the composition of the bacterial and fungal communities present on decomposing fungal necromass from a variety of fungal species, geographic locations, habitats, and incubation times. We found that there is a core group of both bacterial and fungal genera (i.e. a core fungal necrobiome), although the specific size of the core depended on definition. Based on a metric that included both microbial frequency and abundance, we demonstrate that the core is taxonomically and functionally diverse, including bacterial copiotrophs and oligotrophs as well as fungal saprotrophs, ectomycorrhizal fungi, and both fungal and animal parasites. We also show that the composition of the core necrobiome is notably dynamic over time, with many core bacterial and fungal genera having specific associations with the early, middle, or late stages of necromass decomposition. While this study establishes the existence of a core fungal necrobiome, we advocate that profiling the composition of fungal necromass decomposer communities in tropical environments and other terrestrial biomes beyond forests is needed to fill key knowledge gaps regarding the global nature of the fungal necrobiome.
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Affiliation(s)
- Anahi Cantoran
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
| | - François Maillard
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
- Microbial Ecology Group, Department of Biology, Lund University, Naturvetarvägen 22362, Lund, Sweden
| | - Petr Baldrian
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídenská 1083, Prague 142 20, Czech Republic
| | - Peter G Kennedy
- Department of Plant and Microbial Biology, University of Minnesota, 1479 Gortner Avenue, Saint Paul, Minnesota 55108, United States
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2
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De novo metatranscriptomic exploration of gene function in the millipede holobiont. Sci Rep 2022; 12:16173. [PMID: 36171216 PMCID: PMC9519908 DOI: 10.1038/s41598-022-19565-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 08/31/2022] [Indexed: 11/09/2022] Open
Abstract
Invertebrate-microbial associations are widespread in the biosphere and are often related to the function of novel genes, fitness advantages, and even speciation events. Despite ~ 13,000 species of millipedes identified across the world, millipedes and their gut microbiota are markedly understudied compared to other arthropods. Exploring the contribution of individual host-associated microbes is often challenging as many are uncultivable. In this study, we conducted metatranscriptomic profiling of different body segments of a millipede at the holobiont level. This is the first reported transcriptome assembly of a tropical millipede Telodeinopus aoutii (Demange, 1971), as well as the first study on any Myriapoda holobiont. High-throughput RNA sequencing revealed that Telodeinopus aoutii contained > 90% of the core Arthropoda genes. Proteobacteria, Bacteroidetes, Firmicutes, and Euryarchaeota represented dominant and functionally active phyla in the millipede gut, among which 97% of Bacteroidetes and 98% of Firmicutes were present exclusively in the hindgut. A total of 37,831 predicted protein-coding genes of millipede holobiont belonged to six enzyme classes. Around 35% of these proteins were produced by microbiota in the hindgut and 21% by the host in the midgut. Our results indicated that although major metabolic pathways operate at the holobiont level, the involvement of some host and microbial genes are mutually exclusive and microbes predominantly contribute to essential amino acid biosynthesis, short-chain fatty acid metabolism, and fermentation.
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Biodiversity and Metabolic Potential of Bacteria in Bulk Soil from the Peri-Root Zone of Black Alder (Alnus glutinosa), Silver Birch (Betula pendula) and Scots Pine (Pinus sylvestris). Int J Mol Sci 2022; 23:ijms23052633. [PMID: 35269777 PMCID: PMC8910737 DOI: 10.3390/ijms23052633] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
The formation of specific features of forest habitats is determined by the physical, chemical, and biological properties of the soil. The aim of the study was to determine the structural and functional biodiversity of soil microorganisms inhabiting the bulk soil from the peri-root zone of three tree species: Alnus glutinosa, Betula pendula, and Pinus sylvestris. Soil samples were collected from a semi-deciduous forest located in an area belonging to the Agricultural Experimental Station IUNG-PIB in Osiny, Poland. The basic chemical and biological parameters of soils were determined, as well as the structural diversity of bacteria (16S ribosomal RNA (rRNA) sequencing) and the metabolic profile of microorganisms (Biolog EcoPlates). The bulk soils collected from peri-root zone of A. glutinosa were characterized by the highest enzymatic activities. Moreover, the highest metabolic activities on EcoPlates were observed in bulk soil collected in the proximity of the root system the A. glutinosa and B. pendula. In turn, the bulk soil collected from peri-root zone of P. sylvestris had much lower biological activity and a lower metabolic potential. The most metabolized compounds were L-phenylalanine, L-asparagine, D-mannitol, and gamma-hydroxy-butyric acid. The highest values of the diversity indicators were in the soils collected in the proximity of the root system of A. glutinosa and B. pendula. The bulk soil collected from P. sylvestris peri-root zone was characterized by the lowest Shannon’s diversity index. In turn, the evenness index (E) was the highest in soils collected from the P. sylvestris, which indicated significantly lower diversity in these soils. The most abundant classes of bacteria in all samples were Actinobacteria, Acidobacteria_Gp1, and Alphaproteobacteria. The classes Bacilli, Thermoleophilia, Betaproteobacteria, and Subdivision3 were dominant in the B. pendula bulk soil. Streptosporangiales was the most significantly enriched order in the B. pendula soil compared with the A. glutinosa and P. sylvestris. There was a significantly higher mean proportion of aerobic nitrite oxidation, nitrate reduction, sulphate respiration, and sulfur compound respiration in the bulk soil of peri-root zone of A. glutinosa. Our research confirms that the evaluation of soil biodiversity and metabolic potential of bacteria can be of great assistance in a quality and health control tool in the soils of forested areas and in the forest production. Identification of bacteria that promote plant growth and have a high biotechnological potential can be assume a substantial improvement in the ecosystem and use of the forest land.
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García Hernández E, Berg MP, Van Oosten AR, Smit C, Falcão Salles J. Linking Bacterial Communities Associated with the Environment and the Ecosystem Engineer Orchestia gammarellus at Contrasting Salt Marsh Elevations. MICROBIAL ECOLOGY 2021; 82:537-548. [PMID: 33420910 PMCID: PMC8384807 DOI: 10.1007/s00248-020-01656-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
The digestive tract of animals harbors microbiota important for the host's fitness and performance. The interaction between digestive tract bacteria and soil animal hosts is still poorly explored despite the importance of soil fauna for ecosystem processes. In this study, we investigated the interactions between the bacterial communities from the digestive tract of the litter-feeding, semi-terrestrial crustacean Orchestia gammarellus and those obtained from the environment; these organisms thrive in, i.e., soil and plant litter from salt marshes. We hypothesized that elevation is an important driver of soil and litter bacterial communities, which indirectly (via ingested soil and litter bacteria) influences the bacterial communities in the digestive tract of O. gammarellus. Indeed, our results revealed that elevation modulated soil and litter bacterial community composition along with soil organic matter content and the C:N ratio. Soil and plant litter differed in alpha diversity indexes (richness and diversity), and in the case of plant litter, both indexes increased with elevation. In contrast, elevation did not affect the composition of bacterial communities associated with O. gammarellus' digestive tract, suggesting selection by the host, despite the fact that a large component of the bacterial community was also detected in external sources. Importantly, Ca. Bacilloplasma and Vibrio were highly prevalent and abundant in the host. The taxonomic comparison of Ca. Bacilloplasma amplicon sequence variants across the host at different elevations suggested a phylogenetic divergence due to host habitat (i.e., marine or semi-terrestrial), thus supporting their potential functional role in the animal physiology. Our study sheds light on the influence of the environment on soil animal-bacteria interactions and provides insights into the resilience of the O. gammarellus-associated bacteria to increased flooding frequency.
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Affiliation(s)
- Edisa García Hernández
- Microbial Community Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands.
| | - Matty P Berg
- Department of Ecological Sciences, Section Animal Ecology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - A Raoul Van Oosten
- Department of Ecological Sciences, Section Animal Ecology, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Christian Smit
- Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands
| | - Joana Falcão Salles
- Microbial Community Ecology Group, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, Netherlands.
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Shikha D, Singh PK. In situ phytoremediation of heavy metal-contaminated soil and groundwater: a green inventive approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:4104-4124. [PMID: 33210252 DOI: 10.1007/s11356-020-11600-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/09/2020] [Indexed: 05/27/2023]
Abstract
The heavy metal contamination of soil and groundwater is a serious threat to environment worldwide. The survival of human being primarily relies upon soil and groundwater sources. Therefore, the remediation of heavy metal-contaminated soil and groundwater is a matter of utmost concern. Heavy metals are non-degradable and persist in the environment and subsequently contaminate the food chain. Heavy metal pollution puts a serious impact on human health and it adversely affects our physical body. Although, numerous in situ conventional technologies have been utilized for the treatment purpose, but most of the techniques have some limitations such as high cost, deterioration of soil properties, disturbances to soil native flora and fauna and intensive labour. Despite that, in situ phytoremediation is a cost-effective, eco-friendly, solar-driven and novel approach with significant public acceptance. The past research reflects rare discussion addressing both (heavy metal in situ phytoremediation of soil and groundwater) in one platform. The present review article covers both the concepts of in situ phytoremediation of soil and groundwater with major emphasis on health risks of heavy metals, enhanced integrated approaches of in situ phytoremediation, mechanisms of in situ phytoremediation along with effective hyperaccumulator plants for heavy metals remediation, challenges and future prospects.
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Affiliation(s)
- Deep Shikha
- Department of Environmental Science & Engineering, Indian Institute of Technology (IIT; Indian School of Mines), Dhanbad, Jharkhand, 826004, India.
| | - Prasoon Kumar Singh
- Department of Environmental Science & Engineering, Indian Institute of Technology (IIT; Indian School of Mines), Dhanbad, Jharkhand, 826004, India
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Carrias JF, Gerphagnon M, Rodríguez-Pérez H, Borrel G, Loiseau C, Corbara B, Céréghino R, Mary I, Leroy C. Resource availability drives bacterial succession during leaf-litter decomposition in a bromeliad ecosystem. FEMS Microbiol Ecol 2020; 96:5807077. [PMID: 32175561 DOI: 10.1093/femsec/fiaa045] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 03/13/2020] [Indexed: 12/23/2022] Open
Abstract
Despite the growing number of investigations on microbial succession during the last decade, most of our knowledge on primary succession of bacteria in natural environments comes from conceptual models and/or studies of chronosequences. Successional patterns of litter-degrading bacteria remain poorly documented, especially in undisturbed environments. Here we conducted an experiment with tank bromeliads as natural freshwater microcosms to assess major trends in bacterial succession on two leaf-litter species incubated with or without animal exclusion. We used amplicon sequencing and a co-occurrence network to assess changes in bacterial community structure according to treatments. Alpha-diversity and community complexity displayed the same trends regardless of the treatments, highlighting that primary succession of detrital-bacteria is subject to resource limitation and biological interactions, much like macro-organisms. Shifts in bacterial assemblages along the succession were characterized by an increase in uncharacterized taxa and potential N-fixing bacteria, the latter being involved in positive co-occurrence between taxa. These findings support the hypothesis of interdependence between taxa as a significant niche-based process shaping bacterial communities during the advanced stage of succession.
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Affiliation(s)
- Jean-François Carrias
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Mélanie Gerphagnon
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Héctor Rodríguez-Pérez
- UMR EcoFoG, CNRS, CIRAD, INRA, AgroParisTech, Université des Antilles, Université de Guyane, 97310 Kourou, France
| | - Guillaume Borrel
- Institut Pasteur, Department of Microbiology, Unité de Biologie Évolutive de la Cellule Microbienne, Paris, France
| | - Camille Loiseau
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Bruno Corbara
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Régis Céréghino
- Ecolab, Laboratoire Ecologie Fonctionnelle et Environnement, CNRS, Université de Toulouse, 118 route de Narbonne, 31062 Toulouse, France
| | - Isabelle Mary
- Université Clermont-Auvergne, CNRS, LMGE (Laboratoire Microorganismes: Génome et Environnement), F-63000 Clermont-Ferrand, France
| | - Céline Leroy
- UMR EcoFoG, CNRS, CIRAD, INRA, AgroParisTech, Université des Antilles, Université de Guyane, 97310 Kourou, France.,AMAP, IRD, CIRAD, CNRS, INRA, Université Montpellier, Montpellier, France
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Yuan T, McCarthy AJ, Zhang Y, Sekar R. Impact of Temperature, Nutrients and Heavy Metals on Bacterial Diversity and Ecosystem Functioning Studied by Freshwater Microcosms and High-Throughput DNA Sequencing. Curr Microbiol 2020; 77:3512-3525. [PMID: 32740713 DOI: 10.1007/s00284-020-02138-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 07/20/2020] [Indexed: 12/18/2022]
Abstract
Microbial communities are fundamental components in freshwater, and community shifts in ecosystem structure are indicative of changing environmental conditions. This study aimed at investigating the influence of key environmental parameters on bacterial diversity and ecosystem functioning (i.e. organic matter breakdown) in laboratory freshwater microcosms. The effects of varying temperatures (5, 20 and 35 °C), nutrients (representing low, medium and high urbanization) and heavy metals Copper (Cu) and Zinc (Zn) on bacterial diversity and organic matter (OM) breakdown were studied by using leaf bags and capsules filled with polycaprolactonediol-2000 (PCP-2000), respectively. The leaf-associated bacterial diversity was determined by next-generation sequencing of SSU rRNA gene amplicons. The results showed that bacterial diversity increased at high temperature (35 °C) with more operational taxonomic units (OTUs) as compared to medium (20 °C) or low (5 °C) temperatures, whereas nutrient variation had fewer effects on the bacterial community structure. In contrast, the presence of heavy metals, especially high concentrations (100 μM) of Cu, reduced the number of OTUs in the leaf-associated bacterial community. The higher temperatures and nutrient levels accelerated PCP-2000 breakdown rate, but this was impeded by a high concentration (100 μM) of Cu in the short term, though no effect of Zn on breakdown rate was observed. The overall results indicate that temperature and variated heavy metals are among the key factors that affect bacterial diversity and ecosystem functioning in freshwater systems.
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Affiliation(s)
- Tianma Yuan
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, Jiangsu, China
| | - Alan J McCarthy
- Microbiology Research Group, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Yixin Zhang
- Research Center of Environmental Protection and Ecological Restoration Technology, Department of Landscape Architecture, Gold Mantis School of Architecture, Soochow University, Suzhou, Jiangsu, China
| | - Raju Sekar
- Department of Biological Sciences, Xi'an Jiaotong-Liverpool University, Suzhou, 215123, Jiangsu, China.
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Park S, Cho YJ, Jung DY, Jo KN, Lee EJ, Lee JS. Microbial Diversity in Moonmilk of Baeg-nyong Cave, Korean CZO. Front Microbiol 2020; 11:613. [PMID: 32390967 PMCID: PMC7190796 DOI: 10.3389/fmicb.2020.00613] [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: 11/10/2019] [Accepted: 03/19/2020] [Indexed: 11/17/2022] Open
Abstract
The Baeg-nyong cave is a limestone cave which has been nominated as the first critical zone observatory (CZO) in South Korea. Moonmilk is a well-known speleothem composed of various carbonate minerals. To characterize moonmilk from the Baeg-nyong cave, we performed mineralogical analyses and applied high-throughput 16S rRNA gene sequencing to analyze the microbial communities, including bacteria and fungi, of dry and wet moonmilk samples. The results showed that the dry and wet moonmilk samples had different and atypical crystal structures, although they were predominantly composed of CaCO3. Furthermore, metagenomic data revealed that the dry and wet moonmilk samples collected from an oligotrophic environment had completely different bacterial communities when compared to the outside soil, and there was a difference in bacterial communities even between dry and wet moonmilk specimens. Fungal communities, however, did not differ significantly between dry and wet moonmilk samples. This study is the first metagenomic analysis of two different types of moonmilk with different physical properties and the first report on the microbial diversity of moonmilk from a cave in the first CZO in South Korea.
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Affiliation(s)
- Shinae Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea
- Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, South Korea
| | - Yong-Joon Cho
- School of Biological Sciences and Research Institute of Basic Sciences, Seoul National University, Seoul, South Korea
| | - Da-yea Jung
- Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, South Korea
- Division of Geology and Geophysics, College of Natural Sciences, Chuncheon, South Korea
| | - Kyung-nam Jo
- Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, South Korea
- Division of Geology and Geophysics, College of Natural Sciences, Chuncheon, South Korea
| | - Eun-Jin Lee
- Department of Life Sciences, Korea University, Seoul, South Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, South Korea
- Critical Zone Frontier Research Laboratory, Kangwon National University, Chuncheon, South Korea
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9
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Soil Microbial Community Assembly and Interactions Are Constrained by Nitrogen and Phosphorus in Broadleaf Forests of Southern China. FORESTS 2020. [DOI: 10.3390/f11030285] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Subtropical and tropical broadleaf forests play important roles in conserving biodiversity and regulating global carbon cycle. Nonetheless, knowledge about soil microbial diversity, community composition, turnover and microbial functional structure in sub- and tropical broadleaf forests is scarce. In this study, high-throughput sequencing was used to profile soil microbial community composition, and a micro-array GeoChip 5.0 was used to profile microbial functional gene distribution in four sub- and tropical broadleaf forests (HS, MES, HP and JFL) in southern China. The results showed that soil microbial community compositions differed dramatically among all of four forests. Soil microbial diversities in JFL were the lowest (5.81–5.99) and significantly different from those in the other three forests (6.22–6.39). Furthermore, microbial functional gene interactions were the most complex and closest, likely in reflection to stress associated with the lowest nitrogen and phosphorus contents in JFL. In support of the importance of environmental selection, we found selection (78–96%) dominated microbial community assembly, which was verified by partial Mantel tests showing significant correlations between soil phosphorus and nitrogen content and microbial community composition. Taken together, these results indicate that nitrogen and phosphorus are pivotal in shaping soil microbial communities in sub- and tropical broadleaf forests in southern China. Changes in soil nitrogen and phosphorus, in response to plant growth and decomposition, will therefore have significant changes in both microbial community assembly and interaction.
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Albright MBN, Runde A, Lopez D, Gans J, Sevanto S, Woolf D, Dunbar J. Effects of initial microbial biomass abundance on respiration during pine litter decomposition. PLoS One 2020; 15:e0224641. [PMID: 32059014 PMCID: PMC7021309 DOI: 10.1371/journal.pone.0224641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/23/2020] [Indexed: 11/18/2022] Open
Abstract
Microbial biomass is increasingly used to predict respiration in soil organic carbon (SOC) models. Its increased use combined with the difficulty of accurately measuring this variable points a need to directly assess the importance of microbial biomass abundance for carbon (C) cycling. To test the hypothesis that the initial microbial biomass abundance (i.e. biomass abundance on new plant litter) is a strong driver of plant litter C cycling, we manipulated biomass abundance by 10 and 100-fold dilution and composition using 12 source communities on sterile pine litter and measured respiration in microcosms for 30 days. In the first two days of microbial growth on fresh litter, a 100-fold difference in initial biomass abundance caused an average difference in respiration of nearly 300%, but the effect rapidly declined to less than 30% in 10 days and to 14% in 30 days. Parallel simulations with a soil carbon model, SOMIC 1.0, also predicted a 14% difference over 30 days, consistent with the experimental results. Model simulations predicted convergence of cumulative CO2 to within 10% in three months and within 4% in three years. Rapid microbial growth, evidenced by appearance of visible microbial mats on the litter during the first week of incubation, likely attenuates the effects of large initial differences in biomass abundance. In contrast, the persistence of source community as an explanatory factor in driving differences in respiration across microcosms supports the importance of microbial composition in C cycling. Overall, the results suggest that the initial abundance of microbial biomass on litter is a weak driver of C flux from litter decomposition over long timescales (months to years) when litter communities have equal nutrient availability. By extension, slight variation in the timing of microbial dispersal to fresh litter is likely to be a minor factor in long-term C flux.
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Affiliation(s)
- Michaeline B. N. Albright
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
- * E-mail:
| | - Andreas Runde
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Deanna Lopez
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Jason Gans
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Sanna Sevanto
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
| | - Dominic Woolf
- College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States of America
| | - John Dunbar
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America
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11
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Abarca JG, Vargas G, Zuniga I, Whitfield SM, Woodhams DC, Kerby J, McKenzie VJ, Murillo-Cruz C, Pinto-Tomás AA. Assessment of Bacterial Communities Associated With the Skin of Costa Rican Amphibians at La Selva Biological Station. Front Microbiol 2018; 9:2001. [PMID: 30233511 PMCID: PMC6129598 DOI: 10.3389/fmicb.2018.02001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 08/08/2018] [Indexed: 12/15/2022] Open
Abstract
Amphibian skin is a suitable environment for rich communities of microorganisms, both beneficial and detrimental to the host. The amphibian cutaneous microbiota has been hypothesized to play an important role as symbionts, protecting their hosts against disease. Costa Rica has one of the most diverse assemblages of amphibians in the world and we know very little about the microbiota of these tropical animals. For comparison with other studies, we explore the diversity of the skin bacterial communities employing16S rRNA amplicon sequencing of swab samples from twelve species of frogs at La Selva Biological Station in Sarapiquí, Heredia province. The predominant phylum detected in our studies was Proteobacteria, followed by Bacteroidetes and Actinobacteria, with these three phyla representing 89.9% of the total bacterial taxa. At the family level, Sphingobacteriaceae and Comamonadaceae were highly represented among samples. Our results suggest that host species and host family are significant predictors of the variation in microbiota composition. This study helps set the foundation for future research about microbiota composition and resilience to unfavorable conditions, leading to improvement in managing strategies for endangered amphibian species.
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Affiliation(s)
- Juan G. Abarca
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Gabriel Vargas
- Department of the Geophysical Sciences, University of Chicago, Chicago, IL, United States
| | - Ibrahim Zuniga
- Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Steven M. Whitfield
- Department of Conservation and Research, Zoo Miami, Miami, FL, United States
| | - Douglas C. Woodhams
- Department of Biology, University of Massachusetts, Boston, MA, United States
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Jacob Kerby
- Department of Biology, University of South Dakota, Vermillion, SD, United States
| | - Valerie J. McKenzie
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, CO, United States
| | - Catalina Murillo-Cruz
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San Pedro, Costa Rica
| | - Adrián A. Pinto-Tomás
- Centro de Investigación en Estructuras Microscópicas, Universidad de Costa Rica, San Pedro, Costa Rica
- Departamento de Bioquímica, Escuela de Medicina, Universidad de Costa Rica, San Pedro, Costa Rica
- Centro de Investigación en Biología Celular y Molecular, Universidad de Costa Rica, San Pedro, Costa Rica
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12
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Chung DM, Ferree E, Simon DM, Yeh PJ. Patterns of Bird-Bacteria Associations. ECOHEALTH 2018; 15:627-641. [PMID: 29948415 PMCID: PMC6521974 DOI: 10.1007/s10393-018-1342-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 05/15/2018] [Accepted: 05/19/2018] [Indexed: 06/08/2023]
Abstract
Birds, with their broad geographic ranges and close association with humans, have historically played an important role as carriers of human disease and as reservoirs for drug-resistant bacteria. Here, we examine scientific literature over a 15-year timespan to identify reported avian-bacterial associations and factors that may impact zoonotic disease emergence by classifying traits of bird species and their bacteria. We find that the majority of wild birds studied were migratory, in temperate habitats, and in the order Passeriformes. The highest diversity of bacteria was found on birds in natural habitats. The most frequently reported bacteria were Escherichia coli, Salmonella enterica, and Campylobacter jejuni. Of the bacteria species reported, 54% have shown pathogenicity toward humans. Percentage-wise, more pathogens were found in tropical (vs. temperate) habitats and natural (vs. suburban, urban, or agricultural) habitats. Yet, only 22% were tested for antibiotic resistance, and of those tested, 75% of bacteria species were resistant to at least one antibiotic. There were no significant patterns of antibiotic resistance in migratory versus non-migratory birds, temperate versus tropical areas, or different habitats. We discuss biases in detection and representation, and suggest a need for increased sampling in non-temperate zones and in a wider range of avian species.
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Affiliation(s)
- Deanna M Chung
- Department of Ecology and Evolutionary Biology, UCLA, 621 Charles E. Young Drive South, Los Angeles, CA, 90095, USA
| | - Elise Ferree
- Keck Science Department, Claremont McKenna, Scripps and Pitzer Colleges, Claremont, CA, USA
| | - Dawn M Simon
- Department of Biology, University of Nebraska-Kearney, Kearney, NE, USA
| | - Pamela J Yeh
- Department of Ecology and Evolutionary Biology, UCLA, 621 Charles E. Young Drive South, Los Angeles, CA, 90095, USA.
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13
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Hermans SM, Buckley HL, Lear G. Optimal extraction methods for the simultaneous analysis of DNA from diverse organisms and sample types. Mol Ecol Resour 2018; 18:557-569. [DOI: 10.1111/1755-0998.12762] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 01/13/2018] [Accepted: 01/22/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Syrie M. Hermans
- School of Biological Sciences; University of Auckland; Auckland New Zealand
| | - Hannah L. Buckley
- School of Science; Auckland University of Technology; Auckland New Zealand
| | - Gavin Lear
- School of Biological Sciences; University of Auckland; Auckland New Zealand
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14
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Lewin GR, Carlos C, Chevrette MG, Horn HA, McDonald BR, Stankey RJ, Fox BG, Currie CR. Evolution and Ecology of Actinobacteria and Their Bioenergy Applications. Annu Rev Microbiol 2017; 70:235-54. [PMID: 27607553 DOI: 10.1146/annurev-micro-102215-095748] [Citation(s) in RCA: 163] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The ancient phylum Actinobacteria is composed of phylogenetically and physiologically diverse bacteria that help Earth's ecosystems function. As free-living organisms and symbionts of herbivorous animals, Actinobacteria contribute to the global carbon cycle through the breakdown of plant biomass. In addition, they mediate community dynamics as producers of small molecules with diverse biological activities. Together, the evolution of high cellulolytic ability and diverse chemistry, shaped by their ecological roles in nature, make Actinobacteria a promising group for the bioenergy industry. Specifically, their enzymes can contribute to industrial-scale breakdown of cellulosic plant biomass into simple sugars that can then be converted into biofuels. Furthermore, harnessing their ability to biosynthesize a range of small molecules has potential for the production of specialty biofuels.
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Affiliation(s)
- Gina R Lewin
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Camila Carlos
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Marc G Chevrette
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Genetics, University of Wisconsin-Madison, Wisconsin 53706
| | - Heidi A Horn
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706;
| | - Bradon R McDonald
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Robert J Stankey
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
| | - Brian G Fox
- Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726.,Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Wisconsin 53706; .,Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Wisconsin 53726
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15
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Cho H, Kim M, Tripathi B, Adams J. Changes in Soil Fungal Community Structure with Increasing Disturbance Frequency. MICROBIAL ECOLOGY 2017; 74:62-77. [PMID: 28062901 DOI: 10.1007/s00248-016-0919-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Accepted: 12/12/2016] [Indexed: 06/06/2023]
Abstract
Although disturbance is thought to be important in many ecological processes, responses of fungal communities to soil disturbance have been little studied experimentally. We subjected a soil microcosm to physical disturbance, at a range of frequencies designed to simulate ecological disturbance events. We analyzed the fungal community structure using Illumina HiSeq sequencing of the ITS1 region. Fungal diversity was found to decline with the increasing disturbance frequencies, with no sign of the "humpback" pattern found in many studies of larger sedentary organisms. There is thus no evidence of an effect of release from competition resulting from moderate disturbance-which suggests that competition and niche overlap may not be important in limiting soil fungal diversity. Changing disturbance frequency also led to consistent differences in community composition. There were clear differences in OTU-level composition, with different disturbance treatments each having distinct fungal communities. The functional profile of fungal groups (guilds) was changed by the level of disturbance frequency. These predictable differences in community composition suggest that soil fungi can possess different niches in relation to disturbance frequency, or time since last disturbance. Fungi appear to be most abundant relative to bacteria at intermediate disturbance frequencies, on the time scale we studied here.
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Affiliation(s)
- Hyunjun Cho
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, 151-742, South Korea
| | - Mincheol Kim
- Korea Polar Research Institute (KOPRI), Incheon, 460-840, Republic of Korea
| | - Binu Tripathi
- Korea Polar Research Institute (KOPRI), Incheon, 460-840, Republic of Korea
| | - Jonathan Adams
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, 151-742, South Korea.
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16
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Forest Soil Bacteria: Diversity, Involvement in Ecosystem Processes, and Response to Global Change. Microbiol Mol Biol Rev 2017; 81:81/2/e00063-16. [PMID: 28404790 DOI: 10.1128/mmbr.00063-16] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The ecology of forest soils is an important field of research due to the role of forests as carbon sinks. Consequently, a significant amount of information has been accumulated concerning their ecology, especially for temperate and boreal forests. Although most studies have focused on fungi, forest soil bacteria also play important roles in this environment. In forest soils, bacteria inhabit multiple habitats with specific properties, including bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are shaped by nutrient availability and biotic interactions. Bacteria contribute to a range of essential soil processes involved in the cycling of carbon, nitrogen, and phosphorus. They take part in the decomposition of dead plant biomass and are highly important for the decomposition of dead fungal mycelia. In rhizospheres of forest trees, bacteria interact with plant roots and mycorrhizal fungi as commensalists or mycorrhiza helpers. Bacteria also mediate multiple critical steps in the nitrogen cycle, including N fixation. Bacterial communities in forest soils respond to the effects of global change, such as climate warming, increased levels of carbon dioxide, or anthropogenic nitrogen deposition. This response, however, often reflects the specificities of each studied forest ecosystem, and it is still impossible to fully incorporate bacteria into predictive models. The understanding of bacterial ecology in forest soils has advanced dramatically in recent years, but it is still incomplete. The exact extent of the contribution of bacteria to forest ecosystem processes will be recognized only in the future, when the activities of all soil community members are studied simultaneously.
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17
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Contrasting effects of urban habitat complexity on metabolic functional diversity and composition of litter and soil bacterial communities. Urban Ecosyst 2016. [DOI: 10.1007/s11252-016-0617-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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18
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Bordez L, Jourand P, Ducousso M, Carriconde F, Cavaloc Y, Santini S, Claverie JM, Wantiez L, Leveau A, Amir H. Distribution patterns of microbial communities in ultramafic landscape: a metagenetic approach highlights the strong relationships between diversity and environmental traits. Mol Ecol 2016; 25:2258-72. [PMID: 26994404 DOI: 10.1111/mec.13621] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 02/25/2016] [Accepted: 03/15/2016] [Indexed: 11/30/2022]
Abstract
Microbial species richness and assemblages across ultramafic ecosystems were investigated to assess the relationship between their distributional patterns and environmental traits. The structure of microorganism communities in the Koniambo massif, New Caledonia, was investigated using a metagenetic approach correlated with edaphic and floristic factors. Vegetation cover and soil properties significantly shaped the large phylogenetic distribution of operational taxonomic unit within microbial populations, with a mean per habitat of 3.477 (±317) for bacteria and 712 (±43) for fungi. Using variance partitioning, we showed that the effect of aboveground vegetation was the most significant descriptor for both bacterial and fungal communities. The floristic significant predictors explained 43% of the variation for both the bacterial and fungal community structures, while the edaphic significant predictors explained only 32% and 31% of these variations, respectively. These results confirm the previous hypothesis that the distribution of microorganisms was more structured by the vegetation cover rather than the edaphic characteristics and that microbial diversity is not limited in ultramafic ecosystems.
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Affiliation(s)
- L Bordez
- Laboratoire Insulaire du Vivant et de l'Environnement (LIVE), Université de la Nouvelle-Calédonie (UNC), BP R4, Avenue James Cook, 98851, Nouméa Cedex, Nouvelle-Calédonie.,Koniambo Nickel SAS (KNS), BP 696, 98860, Koné, Nouvelle-Calédonie.,IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM, UMR040), TA A-82/J, 34398, Montpellier cedex 5, France.,Institut Agronomique néo-Calédonien (IAC), BPA5, 98848, Nouméa, Nouvelle-Calédonie
| | - P Jourand
- IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM, UMR040), TA A-82/J, 34398, Montpellier cedex 5, France
| | - M Ducousso
- CIRAD, Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM, UMR082), TA A-82/J, 34398, Montpellier cedex 5, France
| | - F Carriconde
- Institut Agronomique néo-Calédonien (IAC), BPA5, 98848, Nouméa, Nouvelle-Calédonie
| | - Y Cavaloc
- Laboratoire Insulaire du Vivant et de l'Environnement (LIVE), Université de la Nouvelle-Calédonie (UNC), BP R4, Avenue James Cook, 98851, Nouméa Cedex, Nouvelle-Calédonie
| | - S Santini
- Laboratoire Information Génomique et Structurale (IGS), UMR7256 CNRS, Aix-Marseille Université, 13288, Marseille cedex 09, France
| | - J M Claverie
- Laboratoire Information Génomique et Structurale (IGS), UMR7256 CNRS, Aix-Marseille Université, 13288, Marseille cedex 09, France
| | - L Wantiez
- Laboratoire Insulaire du Vivant et de l'Environnement (LIVE), Université de la Nouvelle-Calédonie (UNC), BP R4, Avenue James Cook, 98851, Nouméa Cedex, Nouvelle-Calédonie
| | - A Leveau
- Koniambo Nickel SAS (KNS), BP 696, 98860, Koné, Nouvelle-Calédonie
| | - H Amir
- Laboratoire Insulaire du Vivant et de l'Environnement (LIVE), Université de la Nouvelle-Calédonie (UNC), BP R4, Avenue James Cook, 98851, Nouméa Cedex, Nouvelle-Calédonie
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19
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Chen Y, Dai Y, Wang Y, Wu Z, Xie S, Liu Y. Distribution of bacterial communities across plateau freshwater lake and upslope soils. J Environ Sci (China) 2016; 43:61-69. [PMID: 27155410 DOI: 10.1016/j.jes.2015.08.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/23/2015] [Accepted: 08/12/2015] [Indexed: 06/05/2023]
Abstract
Microorganisms are involved in a variety of biogeochemical processes in natural environments. The differences between bacterial communities in freshwaters and upslope soils remain unclear. The present study investigated the bacterial distribution in a plateau freshwater lake, Erhai Lake (southwestern China), and its upslope soils. Illumina MiSeq sequencing illustrated high bacterial diversity in lake sediments and soils. Sediment and soil bacterial communities were mainly composed of Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi and Planctomycetes. However, a distinctive difference in bacterial community structure was found between soil and sediment ecosystems. Water content, nitrogen and pH affected the distribution of the bacterial community across Erhai Lake and its upslope soils. Moreover, the soil bacterial community might also be shaped by plant types. This work could provide some new insights into plateau aquatic and terrestrial microbial ecology.
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Affiliation(s)
- Yihui Chen
- Yunnan Key Laboratory of Pollution Process and Management of Plateau Lake-Watershed, Kunming 650034, China.
| | - Yu Dai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Yilin Wang
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Zhen Wu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China.
| | - Yong Liu
- Key Laboratory of Water and Sediment Sciences (Ministry of Education), College of Environmental Sciences and Engineering, Peking University, Beijing 100871, China
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20
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Zhou G, Zhang J, Zhang C, Feng Y, Chen L, Yu Z, Xin X, Zhao B. Effects of changes in straw chemical properties and alkaline soils on bacterial communities engaged in straw decomposition at different temperatures. Sci Rep 2016; 6:22186. [PMID: 26916902 PMCID: PMC4768159 DOI: 10.1038/srep22186] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 02/03/2016] [Indexed: 12/30/2022] Open
Abstract
Differences in the composition of a bacterial community engaged in decomposing wheat straw in a fluvo-aquic soil at 15 °C, 25 °C, and 35 °C were identified using barcode pyrosequencing. Functional carbon groups in the decomposing wheat straw were evaluated by 13C-NMR (nuclear magnetic resonance). Actinobacteria and Firmicutes were more abundant, whereas Alphaproteobacteria and Bacteroidetes were less abundant, at higher temperatures during the later stages of decomposition. Differences in the chemical properties of straw accounted for 19.3% of the variation in the community composition, whereas soil properties accounted for more (24.0%) and temperature, for less (7.4%). Carbon content of the soil microbial biomass and nitrogen content of straw were significantly correlated with the abundance of Alphaproteobacteria, Actinobacteria, and Bacteroidetes. The chemical properties of straw, especially the NCH/OCH3, alkyl O-C-O, and O-alkyl functional groups, exercised a significant effect on the composition of the bacterial community at different temperatures during decomposition—results that extend our understanding of bacterial communities associated with the decomposition of straw in agro-ecosystems and of the effects of temperature and chemical properties of the decomposing straw and soil on such communities.
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Affiliation(s)
- Guixiang Zhou
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.,Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang 332005, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiabao Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Congzhi Zhang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Youzhi Feng
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Lin Chen
- Institute of Soil and Water Resources and Environmental Science, College of Environmental&Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zhenghong Yu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuli Xin
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Bingzi Zhao
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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21
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Spatiotemporal variation of bacterial and archaeal communities in a pilot-scale constructed wetland for surface water treatment. Appl Microbiol Biotechnol 2015; 100:1479-1488. [DOI: 10.1007/s00253-015-7072-5] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 09/30/2015] [Accepted: 10/06/2015] [Indexed: 01/29/2023]
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22
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Guan W, Yin M, He T, Xie S. Influence of substrate type on microbial community structure in vertical-flow constructed wetland treating polluted river water. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:16202-16209. [PMID: 26263887 DOI: 10.1007/s11356-015-5160-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/04/2015] [Indexed: 06/04/2023]
Abstract
Microorganisms attached on the surfaces of substrate materials in constructed wetland play crucial roles in the removal of organic and inorganic pollutants. However, the impact of substrate material on wetland microbial community structure remains unclear. Moreover, little is known about microbial community in constructed wetland purifying polluted surface water. In this study, Illumina high-throughput sequencing was applied to profile the spatial variation of microbial communities in three pilot-scale surface water constructed wetlands with different substrate materials (sand, zeolite, and gravel). Bacterial community diversity and structure showed remarkable spatial variation in both sand and zeolite wetland systems, but changed slightly in gravel wetland system. Bacterial community was found to be significantly influenced by wetland substrate type. A number of bacterial groups were detected in wetland systems, including Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, Cyanobacteria, Nitrospirae, Planctomycetes, Actinobacteria, Firmicutes, Chlorobi, Spirochaetae, Gemmatimonadetes, Deferribacteres, OP8, WS3, TA06, and OP3, while Proteobacteria (accounting for 29.1-62.3 %), mainly composed of Alpha-, Beta-, Gamma-, and Deltaproteobacteria, showed the dominance and might contribute to the effective reduction of organic pollutants. In addition, Nitrospira-like microorganisms were abundant in surface water constructed wetlands.
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Affiliation(s)
- Wei Guan
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Min Yin
- The Technology Review Center of Shenzhen Habitation and Environment, Shenzhen, 518057, China
| | - Tao He
- South China Institute of Environmental Sciences, Ministry of Environment Protection (MEP), Guangzhou, 510655, China
| | - Shuguang Xie
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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23
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Matulich KL, Martiny JBH. Microbial composition alters the response of litter decomposition to environmental change. Ecology 2015; 96:154-63. [PMID: 26236900 DOI: 10.1890/14-0357.1] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Kecent studies cemonstrate that microorganisms are sensitive to environmental change, and that their community composition influences ecosystem functioning. However, it is unknown whether microbial composition interacts with the environment to affect the response of ecosystem processes to changing abiotic conditions. To investigate the potential for such interactive effects on leaf litter decomposition, we manipulated microbial composition and three environmental factors predicted to change in the future (moisture, nitrogen availability, and temperature). We isolated fungal and bacterial taxa from leaf litter and used them to construct unique communities. Communities were inoculated into microcosms containing sterile leaf litter and exposed to four environmental treatments (control conditions, increased temperature, decreased moisture, and elevated nitrogen availability). Respiration was tracked over 60 days, and communities were pyrosequenced to assess compositional changes. As hypothesized, composition and environmental treatment interacted to influence respiration rates. In particular, microbial composition interacted more strongly with changing nitrogen availability and less so with changing moisture or temperature. Further, the magnitude of a community's response to a particular environmental change was partly. explained by changes in composition over the course of the experiment; microcosms that showed a large change in respiration rate included more taxa whose relative abundance changed as well. Together, these results suggest that information about microbial composition may be more useful for predicting functional responses to some types of environmental changes than others.
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24
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Tardy V, Chabbi A, Charrier X, de Berranger C, Reignier T, Dequiedt S, Faivre-Primot C, Terrat S, Ranjard L, Maron PA. Land Use History Shifts In Situ Fungal and Bacterial Successions following Wheat Straw Input into the Soil. PLoS One 2015; 10:e0130672. [PMID: 26102585 PMCID: PMC4478037 DOI: 10.1371/journal.pone.0130672] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 05/22/2015] [Indexed: 01/04/2023] Open
Abstract
Soil microbial communities undergo rapid shifts following modifications in environmental conditions. Although microbial diversity changes may alter soil functioning, the in situ temporal dynamics of microbial diversity is poorly documented. Here, we investigated the response of fungal and bacterial diversity to wheat straw input in a 12-months field experiment and explored whether this response depended on the soil management history (grassland vs. cropland). Seasonal climatic fluctuations had no effect on the diversity of soil communities. Contrastingly fungi and bacteria responded strongly to wheat regardless of the soil history. After straw incorporation, diversity decreased due to the temporary dominance of a subset of copiotrophic populations. While fungi responded as quickly as bacteria, the resilience of fungal diversity lasted much longer, indicating that the relative involvement of each community might change as decomposition progressed. Soil history did not affect the response patterns, but determined the identity of some of the populations stimulated. Most strikingly, the bacteria Burkholderia, Lysobacter and fungi Rhizopus, Fusarium were selectively stimulated. Given the ecological importance of these microbial groups as decomposers and/or plant pathogens, such regulation of the composition of microbial successions by soil history may have important consequences in terms of soil carbon turnover and crop health.
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Affiliation(s)
| | - Abad Chabbi
- Centre de recherche Poitou-Charentes, INRA, Lusignan, France
| | - Xavier Charrier
- Centre de recherche Poitou-Charentes, INRA, Lusignan, France
| | | | | | - Samuel Dequiedt
- INRA, Plateforme GenoSol, UMR1347 Agroecology, Dijon, France
| | | | | | - Lionel Ranjard
- INRA, UMR 1347 Agroecology, Dijon, France
- INRA, Plateforme GenoSol, UMR1347 Agroecology, Dijon, France
| | - Pierre-Alain Maron
- INRA, UMR 1347 Agroecology, Dijon, France
- INRA, Plateforme GenoSol, UMR1347 Agroecology, Dijon, France
- * E-mail:
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25
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Temporal variation overshadows the response of leaf litter microbial communities to simulated global change. ISME JOURNAL 2015; 9:2477-89. [PMID: 25978544 DOI: 10.1038/ismej.2015.58] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 03/06/2015] [Accepted: 03/13/2015] [Indexed: 01/13/2023]
Abstract
Bacteria and fungi drive the decomposition of dead plant biomass (litter), an important step in the terrestrial carbon cycle. Here we investigate the sensitivity of litter microbial communities to simulated global change (drought and nitrogen addition) in a California annual grassland. Using 16S and 28S rDNA amplicon pyrosequencing, we quantify the response of the bacterial and fungal communities to the treatments and compare these results to background, temporal (seasonal and interannual) variability of the communities. We found that the drought and nitrogen treatments both had significant effects on microbial community composition, explaining 2-6% of total compositional variation. However, microbial composition was even more strongly influenced by seasonal and annual variation (explaining 14-39%). The response of microbial composition to drought varied by season, while the effect of the nitrogen addition treatment was constant through time. These compositional responses were similar in magnitude to those seen in microbial enzyme activities and the surrounding plant community, but did not correspond to a consistent effect on leaf litter decomposition rate. Overall, these patterns indicate that, in this ecosystem, temporal variability in the composition of leaf litter microorganisms largely surpasses that expected in a short-term global change experiment. Thus, as for plant communities, future microbial communities will likely be determined by the interplay between rapid, local background variability and slower, global changes.
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26
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Zhang J, Yang Y, Zhao L, Li Y, Xie S, Liu Y. Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes. Appl Microbiol Biotechnol 2014; 99:3291-302. [PMID: 25432677 DOI: 10.1007/s00253-014-6262-x] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Revised: 11/20/2014] [Accepted: 11/21/2014] [Indexed: 11/30/2022]
Abstract
Both Bacteria and Archaea might be involved in various biogeochemical processes in lacustrine sediment ecosystems. However, the factors governing the intra-lake distribution of sediment bacterial and archaeal communities in various freshwater lakes remain unclear. The present study investigated the sediment bacterial and archaeal communities in 13 freshwater lakes on the Yunnan Plateau. Quantitative PCR assay showed a large variation in bacterial and archaeal abundances. Illumina MiSeq sequencing illustrated high bacterial and archaeal diversities. Bacterial abundance was regulated by sediment total organic carbon and total nitrogen, and water depth, while nitrate nitrogen was an important determinant of bacterial diversity. Proteobacteria, Acidobacteria, Actinobacteria, Bacteroidetes, Chlorobi, Chloroflexi, Cyanobacteria, Firmicutes, Gemmatimonadetes, Nitrospirae, Planctomycetes, and Verrucomicrobia were the major components of sediment bacterial communities. Proteobacteria was the largest phylum, but its major classes and their proportions varied greatly among different lakes, affected by sediment nitrate nitrogen. In addition, both Euryarchaeota and Crenarchaeota were important members in sediment archaeal communities, while unclassified Archaea usually showed the dominance.
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Affiliation(s)
- Jingxu Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
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