1
|
Zhao X, Cui H, Song H, Chen J, Wang J, Liu Z, Ali I, Yang Z, Hou X, Zhou X, Xiao S, Chen S. Contrasting responses of α- and β-multifunctionality to aboveground plant community in the Qinghai-Tibet Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 917:170464. [PMID: 38290671 DOI: 10.1016/j.scitotenv.2024.170464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/01/2024]
Abstract
The aboveground plant communities are crucial in driving ecosystem functioning, particularly being the primary producers in terrestrial ecosystems. Numerous studies have investigated the impacts of aboveground plant communities on multiple ecosystem functions at α-scale. However, such critical effects have been unexplored at β-scale and the comparative assessment of the effects and underlying mechanisms of aboveground plant communities on α- and β-multifunctionality has been lacking. In this study, we examined the effects of aboveground plant communities on soil multifunctionality both at α- and β-scale in the alpine meadow of the Tibetan Plateau. Additionally, we quantified the direct effects of aboveground plant communities, as well as the indirect effects mediated by changes in biotic and abiotic factors, on soil multifunctionality at both scales. Our findings revealed that: 1) Aboveground plant communities had significantly positive effects on α-multifunctionality whereas, β-multifunctionality was not affected significantly. 2) Aboveground plant communities directly influence α- and β-multifunctionality in contrasting ways, with positive and negative effects, respectively. Apart from the direct effects of plant community, we found that soil water content and bacterial β-diversity serving as the primary predictors for the responses of α- and β-multifunctionality to the presence of aboveground plant communities, respectively. And β-soil biodiversity appeared to be a stronger predictor of multifunctionality relative to α-soil biodiversity. Our findings provide novel insights into the drivers of ecosystem multifunctionality at different scales, highlight the importance of maintaining biodiversity at multiple scales and offer valuable knowledge for the maintenance of ecosystem functioning and the restoration of alpine meadow ecosystems.
Collapse
Affiliation(s)
- Xia Zhao
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Hanwen Cui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Hongxian Song
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Jingwei Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Jiajia Wang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Ziyang Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Izhar Ali
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Zi Yang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Xiao Hou
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Xianhui Zhou
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Sa Xiao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China
| | - Shuyan Chen
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu 730000, People's Republic of China.
| |
Collapse
|
2
|
Bontemps Z, Moënne-Loccoz Y, Hugoni M. Stochastic and deterministic assembly processes of microbial communities in relation to natural attenuation of black stains in Lascaux Cave. mSystems 2024; 9:e0123323. [PMID: 38289092 PMCID: PMC10878041 DOI: 10.1128/msystems.01233-23] [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: 11/27/2023] [Accepted: 12/28/2023] [Indexed: 02/21/2024] Open
Abstract
Community assembly processes are complex and understanding them represents a challenge in microbial ecology. Here, we used Lascaux Cave as a stable, confined environment to quantify the importance of stochastic vs deterministic processes during microbial community dynamics across the three domains of life in relation to an anthropogenic disturbance that had resulted in the side-by-side occurrence of a resistant community (unstained limestone), an impacted community (present in black stains), and a resilient community (attenuated stains). Metabarcoding data showed that the microbial communities of attenuated stains, black stains, and unstained surfaces differed, with attenuated stains being in an intermediate position. We found four scenarios to explain community response to disturbance in stable conditions for the three domains of life. Specifically, we proposed the existence of a fourth, not-documented yet scenario that concerns the always-rare microbial taxa, where stochastic processes predominate even after disturbance but are replaced by deterministic processes during post-disturbance recovery. This suggests a major role of always-rare taxa in resilience, perhaps because they might provide key functions required for ecosystem recovery.IMPORTANCEThe importance of stochastic vs deterministic processes in cave microbial ecology has been a neglected topic so far, and this work provided an opportunity to do so in a context related to the dynamics of black-stain alterations in Lascaux, a UNESCO Paleolithic cave. Of particular significance was the discovery of a novel scenario for always-rare microbial taxa in relation to disturbance, in which stochastic processes are replaced later by deterministic processes during post-disturbance recovery, i.e., during attenuation of black stains.
Collapse
Affiliation(s)
- Zélia Bontemps
- UMR 5557 Ecologie Microbienne, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Villeurbanne, France
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratories, Uppsala University, Uppsala, Sweden
| | - Yvan Moënne-Loccoz
- UMR 5557 Ecologie Microbienne, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Villeurbanne, France
| | - Mylène Hugoni
- UMR 5557 Ecologie Microbienne, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Villeurbanne, France
- UMR 5240 Microbiologie Adaptation et Pathogénie, INSA Lyon, CNRS, Université Claude Bernard Lyon 1, Villeurbanne, France
- Institut Universitaire de France (IUF), France
| |
Collapse
|
3
|
Liu Z, Fang J, Song B, Yang Y, Yu Z, Hu J, Dong K, Takahashi K, Adams JM. Stochastic processes dominate soil arbuscular mycorrhizal fungal community assembly along an elevation gradient in central Japan. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 855:158941. [PMID: 36152859 DOI: 10.1016/j.scitotenv.2022.158941] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 09/18/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
Arbuscular mycorrhizal (AM) fungi play an important role in facilitating ecosystem function and stability. Yet, their community response patterns and ecological assembly processes along elevational gradients which cross a range of climates and soil conditions remain elusive. We used Illumina MiSeq sequencing to examine trends in soil AM fungal community along an elevational gradient from 100 m to 2300 m in central Japan. A total of 750 operational taxonomic units (OTUs) affiliated to 12 AM fungal genera were identified from soil samples, and the AM fungal community composition differed strongly with elevation, with variance explained more by climate, followed by soil and plant factors. The AM fungal α-diversity, network connectivity and complexity between AM fungal taxa and also with plant communities all exhibited a maximum at the mid-elevation of 800 m and then declined, principally influenced by soil pH and precipitation. Stochastic processes dominated AM fungal community assembly across the whole elevation gradient, with homogenizing dispersal being the main process. Only when AM fungal communities were contrasted across a relatively broad range of elevations, did variable selection (deterministic process) became significant, and even then in a mixed role with stochasticity. While OTUs of AM fungi are clearly adapted to particular environmental ranges, stochasticity due to rapid dispersal has a major role in determining their occurrence, suggesting that AM fungi may possess generalized and interchangeable niches, and can adjust their distribution rapidly - at least on the scale of a single mountain. This finding emphasizes that the roles of AM fungi in plant ecology may be non-specific and easily substituted, and furthermore that there is rapid local scale dispersal, which may allow plants to maintain effective AM associations under environmental change.
Collapse
Affiliation(s)
- Zihao Liu
- School of Geography and Oceanography, Nanjing University, Nanjing, China
| | - Jie Fang
- School of Geography and Oceanography, Nanjing University, Nanjing, China
| | - Bin Song
- School of Geography and Oceanography, Nanjing University, Nanjing, China
| | - Ying Yang
- School of Geography and Oceanography, Nanjing University, Nanjing, China
| | - Zhi Yu
- Department of Integrative Biotechnology, Sungkyunkwan University, Suwon, South Korea
| | - Junli Hu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Ke Dong
- Life Science Major, Kyonggi University, Suwon, South Korea.
| | - Koichi Takahashi
- Department of Biological Sciences, Shinshu University, Matsumoto, Japan.
| | - Jonathan M Adams
- School of Geography and Oceanography, Nanjing University, Nanjing, China.
| |
Collapse
|
4
|
Microbial Communities in a Serpentinizing Aquifer Are Assembled through Strong Concurrent Dispersal Limitation and Selection. mSystems 2021; 6:e0030021. [PMID: 34519519 PMCID: PMC8547479 DOI: 10.1128/msystems.00300-21] [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] [Indexed: 12/03/2022] Open
Abstract
In recent years, our appreciation of the extent of habitable environments in Earth’s subsurface has greatly expanded, as has our understanding of the biodiversity contained within. Most studies have relied on single sampling points, rather than considering the long-term dynamics of subsurface environments and their microbial populations. One such habitat are aquifers associated with the aqueous alteration of ultramafic rocks through a process known as serpentinization. Ecological modeling performed on a multiyear time series of microbiology, hydrology, and geochemistry in an ultrabasic aquifer within the Coast Range Ophiolite reveals that community assembly is governed by undominated assembly (i.e., neither stochastic [random] nor deterministic [selective] processes alone govern assembly). Controls on community assembly were further assessed by characterizing aquifer hydrogeology and microbial community adaptations to the environment. These analyses show that low permeability rocks in the aquifer restrict the transmission of microbial populations between closely situated wells. Alpha and beta diversity measures and metagenomic and metatranscriptomic data from microbial communities indicate that high pH and low dissolved inorganic carbon levels impose strong environmental selection on microbial communities within individual wells. Here, we find that the interaction between strong selection imposed by extreme pH and enhanced ecological drift due to dispersal limitation imposed by slow fluid flow results in the undominated assembly signal observed throughout the site. Strong environmental selection paired with extremely low dispersal in the subsurface results in low diversity microbial communities that are well adapted to extreme pH conditions and subject to enhanced stochasticity introduced by ecological drift over time. IMPORTANCE Microbial communities existing under extreme or stressful conditions have long been thought to be structured primarily by deterministic processes. The application of macroecology theory and modeling to microbial communities in recent years has spurred assessment of assembly processes in microbial communities, revealing that both stochastic and deterministic processes are at play to different extents within natural environments. We show that low diversity microbial communities in a hard-rock serpentinizing aquifer are assembled under the influence of strong selective processes imposed by high pH and enhanced ecological drift that occurs as the result of dispersal limitation due to the slow movement of water in the low permeability aquifer. This study demonstrates the important roles that both selection and dispersal limitation play in terrestrial serpentinites, where extreme pH assembles a microbial metacommunity well adapted to alkaline conditions and dispersal limitation drives compositional differences in microbial community composition between local communities in the subsurface.
Collapse
|
5
|
Song X, Song J, Yan Q, Zhou J, Cai Z. Assembly of a Benthic Microbial Community in a Eutrophic Bay with a Long History of Oyster Culturing. Microorganisms 2021; 9:microorganisms9102019. [PMID: 34683340 PMCID: PMC8536970 DOI: 10.3390/microorganisms9102019] [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: 09/02/2021] [Revised: 09/11/2021] [Accepted: 09/14/2021] [Indexed: 11/27/2022] Open
Abstract
The introduction of oysters to a waterbody is an efficient method for decreasing levels of eutrophication. Oysters affect sedimental environments and benthic microbes via their roles in nutrient cycling. However, little is known about how long-term oyster culturing affects benthic microbial community assembly. In the present study, top and bottom sediments from an oyster-culture area and non-culture area, in a eutrophic bay with a long history of oyster culturing, were obtained for environmental parameter measurement and microbe identification. Deterministic and stochastic processes in microbial community assembly were assessed. In particular, keystone species identification through network analysis was combined with measured environmental parameters to determine the factors related to community assembly processes. Our results suggest that oyster culturing relates to greater variation in both biological and non-biological sediment profiles. In benthic communities, Proteobacteria and Chloroflexi were the most abundant phyla, and community compositions were significantly different between sample groups. We also found that community assembly was more affected by deterministic factors than stochastic ones, when oysters were present. Moisture, or water content, and pH were identified as affecting deterministic and stochastic processes, respectively, but only water content was a driver associated with oyster culturing. Additionally, although keystone species presented a similar pattern of composition to peripheral species, they responded to their environments differently. Furthermore, model selection, fitting keystone species to community assembly processes, indicates their role in shaping microbial communities.
Collapse
Affiliation(s)
- Xiao Song
- School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.S.); (J.S.); (Q.Y.)
- Shenzhen Public Platform of Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
| | - Junting Song
- School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.S.); (J.S.); (Q.Y.)
- Shenzhen Public Platform of Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
| | - Qi Yan
- School of Life Sciences, Tsinghua University, Beijing 100084, China; (X.S.); (J.S.); (Q.Y.)
- Shenzhen Public Platform of Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
| | - Jin Zhou
- Shenzhen Public Platform of Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
| | - Zhonghua Cai
- Shenzhen Public Platform of Screening and Application of Marine Microbial Resources, The Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China;
- Correspondence:
| |
Collapse
|
6
|
Zhou X, Khashi U Rahman M, Liu J, Wu F. Soil acidification mediates changes in soil bacterial community assembly processes in response to agricultural intensification. Environ Microbiol 2021; 23:4741-4755. [PMID: 34289203 PMCID: PMC9291526 DOI: 10.1111/1462-2920.15675] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 12/13/2022]
Abstract
Agricultural intensification is known to alter the assembly of soil microbial communities, which regulate several critical ecosystem processes. However, the underlying ecological processes driving changes in microbial community assembly, particularly at the regional scale, remain poorly understood. Using 16S rDNA sequencing, we characterized soil bacterial community assembly in three land‐use types with increasing land‐use intensity: open fields cultivated with main crops (CF) or vegetables (VF), and greenhouses cultivated with vegetables (VG). Compared with CF, VF and VG altered bacterial community composition and decreased spatial turnover rates of edaphic variables and bacterial communities. Bacterial community assembly was primarily governed by deterministic processes; however, bacterial communities in VF and VG were phylogenetically less clustered and more influenced by variable selection and less by dispersal limitation. Soil pH was the most important edaphic variable mediating the changes in bacterial community assembly processes induced by agricultural intensification. Specifically, decreasing soil pH led to stochastic assembly of bacterial community. Soil pH was lower in more intensively managed lands, especially in case of VG (pH range: 5.86–7.42). Overall, agricultural intensification altered soil bacterial community assembly processes, which was associated with soil acidification. These findings may have implications for improving soil quality and agroecosystem sustainability.
Collapse
Affiliation(s)
- Xingang Zhou
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China.,Department of Horticulture, Northeast Agricultural University, Harbin, 150030, China
| | | | - Junjie Liu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Fengzhi Wu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Northeast Region), Ministry of Agriculture and Rural Affairs, Northeast Agricultural University, Harbin, 150030, China.,Department of Horticulture, Northeast Agricultural University, Harbin, 150030, China
| |
Collapse
|
7
|
Dickey JR, Swenie RA, Turner SC, Winfrey CC, Yaffar D, Padukone A, Beals KK, Sheldon KS, Kivlin SN. The Utility of Macroecological Rules for Microbial Biogeography. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.633155] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Macroecological rules have been developed for plants and animals that describe large-scale distributional patterns and attempt to explain the underlying physiological and ecological processes behind them. Similarly, microorganisms exhibit patterns in relative abundance, distribution, diversity, and traits across space and time, yet it remains unclear the extent to which microorganisms follow macroecological rules initially developed for macroorganisms. Additionally, the usefulness of these rules as a null hypothesis when surveying microorganisms has yet to be fully evaluated. With rapid advancements in sequencing technology, we have seen a recent increase in microbial studies that utilize macroecological frameworks. Here, we review and synthesize these macroecological microbial studies with two main objectives: (1) to determine to what extent macroecological rules explain the distribution of host-associated and free-living microorganisms, and (2) to understand which environmental factors and stochastic processes may explain these patterns among microbial clades (archaea, bacteria, fungi, and protists) and habitats (host-associated and free living; terrestrial and aquatic). Overall, 78% of microbial macroecology studies focused on free living, aquatic organisms. In addition, most studies examined macroecological rules at the community level with only 35% of studies surveying organismal patterns across space. At the community level microorganisms often tracked patterns of macroorganisms for island biogeography (74% confirm) but rarely followed Latitudinal Diversity Gradients (LDGs) of macroorganisms (only 32% confirm). However, when microorganisms and macroorganisms shared the same macroecological patterns, underlying environmental drivers (e.g., temperature) were the same. Because we found a lack of studies for many microbial groups and habitats, we conclude our review by outlining several outstanding questions and creating recommendations for future studies in microbial ecology.
Collapse
|
8
|
Liao H, Li C, Ai Y, Kou Y. Gut microbiome is more stable in males than in females during the development of colorectal cancer. J Appl Microbiol 2020; 131:435-448. [PMID: 33245828 DOI: 10.1111/jam.14943] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/13/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022]
Abstract
AIMS Gut microbial alterations have great potential to predict the development of colorectal cancer (CRC); however, how gut microbes respond to the development of CRC in males and females at the community level is unknown. We aim to investigate the differences of gut microbiota between the male and female. METHODS AND RESULTS We reanalysed the dataset in a published project from a sex perspective at the community level by characterizing the gut microbiome in patients (including males and females) from three clinical groups representative of the stages of CRC development: healthy, adenoma, and carcinoma. The results indicated that the microbial α-diversity showed no significant difference in the male gut but had decreased significantly in the female gut with the development of CRC. In males, a significant difference in the microbial β-diversity was only observed between the healthy and carcinoma subgroups. However, significant community deviations were detected with the development of CRC in females. The microbial community assembly processes changed from deterministic to stochastic in males, whereas they became increasingly deterministic in females with the development of CRC. Moreover microbial co-occurrence associations tended to be more complicated in males; rare species were enriched in the co-occurrence network of the male gut, whereas key species loss was observed in the co-occurrence network of the female gut. CONCLUSIONS The microbial communities in the male gut were more stable than those in the female gut, and microbial community assembly in the gut was sex dependent with the development of CRC. Our study suggests that sexual dimorphism needs to be considered to better predict the risk of CRC based on microbial shifts. SIGNIFICANCE AND IMPACT OF THE STUDY To the best of our knowledge, this is the first report showing how gut microbes respond to the development of CRC in males and females at the community scale.
Collapse
Affiliation(s)
- H Liao
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - C Li
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Y Ai
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Science, Sichuan University, Chengdu, China
| | - Y Kou
- Key Laboratory of Environmental and Applied Microbiology, Chinese Academy of Sciences, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| |
Collapse
|
9
|
Homogeneous environmental selection dominates microbial community assembly in the oligotrophic South Pacific Gyre. Mol Ecol 2020; 29:4680-4691. [DOI: 10.1111/mec.15651] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 09/06/2020] [Accepted: 09/08/2020] [Indexed: 01/04/2023]
|
10
|
Silva MOD, Pernthaler J. Biomass addition alters community assembly in ultrafiltration membrane biofilms. Sci Rep 2020; 10:11552. [PMID: 32665605 PMCID: PMC7360762 DOI: 10.1038/s41598-020-68460-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/15/2020] [Indexed: 11/25/2022] Open
Abstract
Freshwater biofilms assemble from a pool of rare water column genotypes. Random density fluctuations and temporal species turnover of functionally equivalent potential colonizers result in compositional variability of newly formed biofilm communities. We hypothesized that stronger environmental filtering as induced by enhanced substrate levels might reduce the impact of a locally variable pool of colonizers and instead select for more universal habitat specialists. Our model were heterotrophic biofilms that form on membranes during gravity-driven ultrafiltration of lake water. In four separate experiments, biomass of the cyanobacterium Microcystis was added to the feed water of one set of treatments (BM) and the resulting biofilm communities were compared to unamended controls (CTRL). Biomass addition led to a significant shift of community assembly processes: Replicate BM biofilms were more similar to each other than by chance in 3 of 4 experiments, whereas the opposite was the case for CTRL communities. Moreover, BM communities were more stochastically assembled across experiments from a common 'regional' pool of biofilm colonizers, whereas the composition of CTRL communities was mainly determined by experiment-specific 'local' genotypes. Interestingly, community assembly processes were also related to both, physiology (aerobic vs. anaerobic lifestyle) and the phylogenetic affiliation of biofilm bacteria.
Collapse
Affiliation(s)
- Marisa O D Silva
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland.
| |
Collapse
|
11
|
Zhou J, Nelson TM, Rodriguez Lopez C, Sarma RR, Zhou SJ, Rollins LA. A comparison of nonlethal sampling methods for amphibian gut microbiome analyses. Mol Ecol Resour 2020; 20:844-855. [PMID: 31990452 DOI: 10.1111/1755-0998.13139] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 12/03/2019] [Accepted: 01/20/2020] [Indexed: 12/27/2022]
Abstract
Noninvasive sampling methods for studying intestinal microbiomes are widely applied in studies of endangered species and in those conducting temporal monitoring during manipulative experiments. Although existing studies show that noninvasive sampling methods among different taxa vary in their accuracy, no studies have yet been published comparing nonlethal sampling methods in adult amphibians. In this study, we compare microbiomes from two noninvasive sample types (faeces and cloacal swabs) to that of the large intestine in adult cane toads, Rhinella marina. We use 16S rRNA gene sequencing to investigate how microbial communities change along the digestive tract and which nonlethal sampling method better represents large intestinal microbiota. We found that cane toads' intestinal microbiota was dominated by Bacteroidetes, Proteobacteria and Firmicutes and, interestingly, we also saw a high proportion of Fusobacteria, which has previously been associated with marine species and changes in frog immunity. The large and small intestine of cane toads had a similar microbial composition, but the large intestine showed higher diversity. Our results indicate that cloacal swabs were more similar to large intestine samples than were faecal samples, and small intestine samples were significantly different from both nonlethal sample types. Our study provides valuable information for future investigations of the cane toad gut microbiome and validates the use of cloacal swabs as a nonlethal method to study changes in the large intestine microbiome. These data provide insights for future studies requiring nonlethal sampling of amphibian gut microbiota.
Collapse
Affiliation(s)
- Jia Zhou
- School of Agriculture, Food and Wine, University of Adelaide, SA, Glen Osmond, Australia
| | - Tiffanie Maree Nelson
- Queensland Facility for Advanced Bioinformatics, School of Medicine, Menzies Health Institute Queensland, Griffith University, Southport, Qld, Australia
| | - Carlos Rodriguez Lopez
- Environmental Epigenetics and Genetics Group, Department of Horticulture, College of Agriculture, Food and Environment, University of Kentucky, Lexington, KY, USA
| | - Roshmi Rekha Sarma
- School of Biological, Earth and Environmental Sciences, Ecology & Evolution Research Centre, Biological Sciences South (E26) UNSW, University of New South Wales, Kensington, NSW, Australia
| | - Shao Jia Zhou
- School of Agriculture, Food and Wine, University of Adelaide, SA, Glen Osmond, Australia
| | - Lee Ann Rollins
- School of Biological, Earth and Environmental Sciences, Ecology & Evolution Research Centre, Biological Sciences South (E26) UNSW, University of New South Wales, Kensington, NSW, Australia
| |
Collapse
|
12
|
Sheng Y, Cong W, Yang L, Liu Q, Zhang Y. Forest Soil Fungal Community Elevational Distribution Pattern and Their Ecological Assembly Processes. Front Microbiol 2019; 10:2226. [PMID: 31636612 PMCID: PMC6787267 DOI: 10.3389/fmicb.2019.02226] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/11/2019] [Indexed: 11/17/2022] Open
Abstract
Soil fungi play vital roles in natural ecosystems, however, their community distribution patterns along different environmental gradients and ecological assembly processes remain unclear. In this study, Illumina MiSeq sequencing was used to investigate the soil fungal community structures of five different forest types along an elevational gradient, and a framework based on a null model was adopted to quantify the relative contribution of deterministic and stochastic ecological assembly processes. The results showed that the majority of soil fungal OTUs were derived from Zygomycota, Basidiomycota, and Ascomycota. Soil fungal community structure differed significantly among the five sites (P < 0.01), and the fungal α-diversity decreased as elevation increased (P < 0.01). The null model showed that the relative contribution of stochastic processes (37.78-73.33%) was higher than that of deterministic processes (26.67-62.22%) within the same forest type, while that of deterministic processes (35.00-93.00%) was higher than stochastic processes (7.00-65.00%) between forest types. These results suggest that forest soil fungal diversity decreased significantly with increasing elevation, and that deterministic processes may be key factors influencing soil fungal community assemblies among forest types. The results of this study provide new insight into soil fungal distribution patterns and community assembly processes in natural forest ecosystems.
Collapse
Affiliation(s)
- Yuyu Sheng
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, and the Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Beijing, China
| | - Wei Cong
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, and the Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Beijing, China
| | - Linsen Yang
- Shennongjia National Park Administration, and Hubei Provincial Key Laboratory on Conservation Biology of the Shennongjia Golden Monkey, Shennongjia, China
| | - Qiang Liu
- Shennongjia National Park Administration, and Hubei Provincial Key Laboratory on Conservation Biology of the Shennongjia Golden Monkey, Shennongjia, China
| | - Yuguang Zhang
- Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, and the Key Laboratory of Biological Conservation of National Forestry and Grassland Administration, Beijing, China
| |
Collapse
|
13
|
Lee TK, Han I, Kim MS, Seong HJ, Kim JS, Sul WJ. Characterization of a nifH-Harboring Bacterial Community in the Soil-Limited Gotjawal Forest. Front Microbiol 2019; 10:1858. [PMID: 31456776 PMCID: PMC6700220 DOI: 10.3389/fmicb.2019.01858] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 07/29/2019] [Indexed: 11/13/2022] Open
Abstract
Using a high-throughput metagenomic approach, we evaluated nifH-harboring bacterial communities and their assembly in the Gotjawal forest, which was naturally formed on basalt rocks with thin layer of soil. Significant differences in soil properties and community structure were observed in comparison with similar communities in various habitats, including other lava-formed forests (on Jeju Island and in Hawaii) and in regions with high humidity (Florida) or low temperatures (Alaska). nifH-harboring bacterial communities were found to assemble along gradients of environmental factors, particularly cation-exchange capacity. Unlike in other regions, in the Gotjawal forest, Paenibacillus and Clostridium, which belong to the phylum Firmicutes, were present in significantly higher proportion than in other regions. Network analysis suggested that much fewer co-occurrence relationships occurred in the Gotjawal forest than in other lava-formed forests. Our results indicate that the unique nifH-harboring bacterial community and its assembly in the Gotjawal forest are due to its distinctive soil properties, which has implications for microbial interactions and functional potentials.
Collapse
Affiliation(s)
- Tae Kwon Lee
- Department of Environmental Engineering, Yonsei University, Wonju, South Korea
| | - Il Han
- Department of Environmental Engineering, Yonsei University, Wonju, South Korea
| | - Min Sung Kim
- Department of Environmental Engineering, Yonsei University, Wonju, South Korea
| | - Hoon Je Seong
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Jong-Shik Kim
- Marine Industry Research Institute for East Sea Rim, Uljin, South Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| |
Collapse
|
14
|
Langenheder S, Lindström ES. Factors influencing aquatic and terrestrial bacterial community assembly. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:306-315. [PMID: 30618071 DOI: 10.1111/1758-2229.12731] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/26/2018] [Indexed: 05/12/2023]
Abstract
During recent years, many studies have shown that different processes including drift, environmental selection and dispersal can be important for the assembly of bacterial communities in aquatic and terrestrial ecosystems. However, we lack a conceptual overview about the ecological context and factors that influence the relative importance of the different assembly mechanisms and determine their dynamics in time and space. Focusing on free-living, i.e., nonhost associated, bacterial communities, this minireview, therefore, summarizes and conceptualizes findings from empirical studies about how (i) environmental factors, such as environmental heterogeneity, disturbances, productivity and trophic interactions; (ii) connectivity and dispersal rates (iii) spatial scale, (iv) community properties and traits and (v) the use of taxonomic/phylogenetic or functional metrics influence the relative importance of different community assembly processes. We find that there is to-date little consistency among studies and suggest that future studies should now address how (i)-(v) differ between habitats and organisms and how this, in turn, influences the temporal and spatial-scale dependency of community assembly processes in microorganisms.
Collapse
Affiliation(s)
- Silke Langenheder
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| | - Eva S Lindström
- Department of Ecology and Genetics/Limnology, Uppsala University, Norbyvägen 18D, 75236 Uppsala, Sweden
| |
Collapse
|
15
|
Fiddler crab bioturbation determines consistent changes in bacterial communities across contrasting environmental conditions. Sci Rep 2019; 9:3749. [PMID: 30842580 PMCID: PMC6403291 DOI: 10.1038/s41598-019-40315-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/08/2019] [Indexed: 11/25/2022] Open
Abstract
Ecosystem functions are regulated by compositional and functional traits of bacterial communities, shaped by stochastic and deterministic processes. Biogeographical studies have revealed microbial community taxonomy in a given ecosystem to change alongside varying environmental characteristics. Considering that stable functional traits are essential for community stability, we hypothesize that contrasting environmental conditions affect microbial taxonomy rather than function in a model system, testing this in three geographically distinct mangrove forests subjected to intense animal bioturbation (a shared deterministic force). Using a metabarcoding approach combined with sediment microprofiling and biochemistry, we examined vertical and radial sediment profiles of burrows belonging to the pantropical fiddler crab (subfamily Gelasiminae) in three contrasting mangrove environments across a broad latitudinal range (total samples = 432). Each mangrove was environmentally distinct, reflected in taxonomically different bacterial communities, but communities consistently displayed the same spatial stratification (a halo effect) around the burrow which invariably determined the retention of similar inferred functional community traits independent of the local environment.
Collapse
|
16
|
Lupatini M, Suleiman AKA, Jacques RJS, Lemos LN, Pylro VS, Van Veen JA, Kuramae EE, Roesch LFW. Moisture Is More Important than Temperature for Assembly of Both Potentially Active and Whole Prokaryotic Communities in Subtropical Grassland. MICROBIAL ECOLOGY 2019; 77:460-470. [PMID: 30607437 DOI: 10.1007/s00248-018-1310-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 12/18/2018] [Indexed: 06/09/2023]
Abstract
Moisture and temperature play important roles in the assembly and functioning of prokaryotic communities in soil. However, how moisture and temperature regulate the function of niche- versus neutral-based processes during the assembly of these communities has not been examined considering both the total microbial community and the sole active portion with potential for growth in native subtropical grassland. We set up a well-controlled microcosm-based experiment to investigate the individual and combined effects of moisture and temperature on soil prokaryotic communities by simulating subtropical seasons in grassland. The prokaryotic populations with potential for growth and the total prokaryotic community were assessed by 16S rRNA transcript and 16S rRNA gene analyses, respectively. Moisture was the major factor influencing community diversity and structure, with a considerable effect of this factor on the total community. The prokaryotic populations with potential for growth and the total communities were influenced by the same assembly rules, with the niche-based mechanism being more influential in communities under dry condition. Our results provide new information regarding moisture and temperature in microbial communities of soil and elucidate how coexisting prokaryotic populations, under different physiological statuses, are shaped in native subtropical grassland soil.
Collapse
Affiliation(s)
- Manoeli Lupatini
- Departamento de Solos, Programa de Pós-graduação em Ciência do Solo, Universidade Federal de Santa Maria, Roraima, 1000, Santa Maria, 97105-900, Brazil
| | - Afnan K A Suleiman
- Departamento de Solos, Programa de Pós-graduação em Ciência do Solo, Universidade Federal de Santa Maria, Roraima, 1000, Santa Maria, 97105-900, Brazil
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Rodrigo J S Jacques
- Departamento de Solos, Programa de Pós-graduação em Ciência do Solo, Universidade Federal de Santa Maria, Roraima, 1000, Santa Maria, 97105-900, Brazil
| | - Leandro N Lemos
- Laboratório de Biologia Molecular e Celular, Centro de Energia Nuclear na Agricultura CENA, Universidade de São Paulo USP, Piracicaba, SP, Brazil
| | - Victor S Pylro
- Department of Biology, Federal University of Lavras - UFLA, Lavras, Minas Gerais, Brazil
| | - Johannes A Van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Luiz F W Roesch
- Centro Interdisciplinar de Pesquisas em Biotecnologia - CIP-Biotec, Universidade Federal do Pampa, Campus São Gabriel, Avenida Antonio Trilha, 1847, São Gabriel, 97300-000, Brazil.
| |
Collapse
|
17
|
Tripathi BM, Stegen JC, Kim M, Dong K, Adams JM, Lee YK. Soil pH mediates the balance between stochastic and deterministic assembly of bacteria. ISME JOURNAL 2018. [PMID: 29515169 PMCID: PMC5864241 DOI: 10.1038/s41396-018-0082-4] [Citation(s) in RCA: 373] [Impact Index Per Article: 62.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Little is known about the factors affecting the relative influences of stochastic and deterministic processes that govern the assembly of microbial communities in successional soils. Here, we conducted a meta-analysis of bacterial communities using six different successional soil datasets distributed across different regions. Different relationships between pH and successional age across these datasets allowed us to separate the influences of successional age (i.e., time) from soil pH. We found that extreme acidic or alkaline pH conditions lead to assembly of phylogenetically more clustered bacterial communities through deterministic processes, whereas pH conditions close to neutral lead to phylogenetically less clustered bacterial communities with more stochasticity. We suggest that the influence of pH, rather than successional age, is the main driving force in producing trends in phylogenetic assembly of bacteria, and that pH also influences the relative balance of stochastic and deterministic processes along successional soils. Given that pH had a much stronger association with community assembly than did successional age, we evaluated whether the inferred influence of pH was maintained when studying globally distributed samples collected without regard for successional age. This dataset confirmed the strong influence of pH, suggesting that the influence of soil pH on community assembly processes occurs globally. Extreme pH conditions likely exert more stringent limits on survival and fitness, imposing strong selective pressures through ecological and evolutionary time. Taken together, these findings suggest that the degree to which stochastic vs. deterministic processes shape soil bacterial community assembly is a consequence of soil pH rather than successional age.
Collapse
Affiliation(s)
- Binu M Tripathi
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - James C Stegen
- Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, WA, 99352, USA
| | - Mincheol Kim
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea
| | - Ke Dong
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jonathan M Adams
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK.
| | - Yoo Kyung Lee
- Korea Polar Research Institute, Incheon, 21990, Republic of Korea.
| |
Collapse
|
18
|
Shen D, Jürgens K, Beier S. Experimental insights into the importance of ecologically dissimilar bacteria to community assembly along a salinity gradient. Environ Microbiol 2018; 20:1170-1184. [DOI: 10.1111/1462-2920.14059] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Revised: 12/18/2017] [Accepted: 01/27/2018] [Indexed: 11/29/2022]
Affiliation(s)
- Dandan Shen
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Department of Biological Oceanography, Seestr. 15; D-18119 Rostock Germany
| | - Klaus Jürgens
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Department of Biological Oceanography, Seestr. 15; D-18119 Rostock Germany
| | - Sara Beier
- Leibniz Institute for Baltic Sea Research Warnemünde (IOW), Department of Biological Oceanography, Seestr. 15; D-18119 Rostock Germany
| |
Collapse
|
19
|
Larson CA, Adumatioge L, Passy SI. The number of limiting resources in the environment controls the temporal diversity patterns in the algal benthos. MICROBIAL ECOLOGY 2016; 72:64-69. [PMID: 26943146 DOI: 10.1007/s00248-016-0741-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 02/15/2016] [Indexed: 06/05/2023]
Abstract
The role of the number of limiting resources (NLR) on species richness has been the subject of much theoretical and experimental work. However, how the NLR controls temporal beta diversity and the processes of community assembly is not well understood. To address this knowledge gap, we initiated a series of laboratory microcosm experiments, exposing periphyton communities to a gradient of NLR from 0 to 3, generated by supplementation with nitrogen, phosphorus, iron, and all their combinations. We hypothesized that similarly to alpha diversity, shown to decrease with the NLR in benthic algae, temporal beta diversity would also decline due to filtering. Additionally, we predicted that the NLR would also affect turnover and community nestedness, which would show opposing responses. Indeed, as the NLR increased, temporal beta diversity decreased; turnover, indicative of competition, decreased; and nestedness, suggestive of complementarity, increased. Finally, the NLR determined the role of deterministic versus stochastic processes in community assembly, showing respectively an increasing and a decreasing trend. These results imply that the NLR has a much greater, yet still unappreciated influence on producer communities, constraining not only alpha diversity but also temporal dynamics and community assembly.
Collapse
Affiliation(s)
- Chad A Larson
- Washington State Department of Ecology, Environmental Assessment Program, 300 Desmond Drive SE, Lacey, WA, 98503, USA.
| | - Larry Adumatioge
- Biology Department, The University of Texas at Arlington, Box 19498, Arlington, TX, 76019-0498, USA
| | - Sophia I Passy
- Biology Department, The University of Texas at Arlington, Box 19498, Arlington, TX, 76019-0498, USA.
| |
Collapse
|
20
|
Environmental Disturbances Decrease the Variability of Microbial Populations within Periphyton. mSystems 2016; 1:mSystems00013-16. [PMID: 27822539 PMCID: PMC5072133 DOI: 10.1128/msystems.00013-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/19/2016] [Indexed: 11/30/2022] Open
Abstract
There are many reasons why microbial community composition is difficult to model. For example, the high diversity and high rate of change of these communities make it challenging to identify causes of community turnover. Furthermore, the processes that shape community composition can be either deterministic, which cause communities to converge upon similar compositions, or stochastic, which increase variability in community composition. However, modeling microbial community composition is possible only if microbes show repeatable responses to extrinsic forcing. In this study, we hypothesized that environmental stress acts as a deterministic force that shapes microbial community composition. Other studies have investigated if disturbances can alter microbial community composition, but relatively few studies ask about the repeatability of the effects of disturbances. Mechanistic models implicitly assume that communities show consistent responses to stressors; here, we define and quantify microbial variability to test this assumption. A central pursuit of microbial ecology is to accurately model changes in microbial community composition in response to environmental factors. This goal requires a thorough understanding of the drivers of variability in microbial populations. However, most microbial ecology studies focus on the effects of environmental factors on mean population abundances, rather than on population variability. Here, we imposed several experimental disturbances upon periphyton communities and analyzed the variability of populations within disturbed communities compared with those in undisturbed communities. We analyzed both the bacterial and the diatom communities in the periphyton under nine different disturbance regimes, including regimes that contained multiple disturbances. We found several similarities in the responses of the two communities to disturbance; all significant treatment effects showed that populations became less variable as the result of environmental disturbances. Furthermore, multiple disturbances to these communities were often interactive, meaning that the effects of two disturbances could not have been predicted from studying single disturbances in isolation. These results suggest that environmental factors had repeatable effects on populations within microbial communities, thereby creating communities that were more similar as a result of disturbances. These experiments add to the predictive framework of microbial ecology by quantifying variability in microbial populations and by demonstrating that disturbances can place consistent constraints on the abundance of microbial populations. Although models will never be fully predictive due to stochastic forces, these results indicate that environmental stressors may increase the ability of models to capture microbial community dynamics because of their consistent effects on microbial populations. IMPORTANCE There are many reasons why microbial community composition is difficult to model. For example, the high diversity and high rate of change of these communities make it challenging to identify causes of community turnover. Furthermore, the processes that shape community composition can be either deterministic, which cause communities to converge upon similar compositions, or stochastic, which increase variability in community composition. However, modeling microbial community composition is possible only if microbes show repeatable responses to extrinsic forcing. In this study, we hypothesized that environmental stress acts as a deterministic force that shapes microbial community composition. Other studies have investigated if disturbances can alter microbial community composition, but relatively few studies ask about the repeatability of the effects of disturbances. Mechanistic models implicitly assume that communities show consistent responses to stressors; here, we define and quantify microbial variability to test this assumption. Author Video: An author video summary of this article is available.
Collapse
|
21
|
Miyambo T, Makhalanyane TP, Cowan DA, Valverde A. Plants of the fynbos biome harbour host species-specific bacterial communities. FEMS Microbiol Lett 2016; 363:fnw122. [DOI: 10.1093/femsle/fnw122] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2016] [Indexed: 12/28/2022] Open
|
22
|
Pereira LB, Vicentini R, Ottoboni LMM. Characterization of the core microbiota of the drainage and surrounding soil of a Brazilian copper mine. Genet Mol Biol 2015; 38:484-9. [PMID: 26537607 PMCID: PMC4763313 DOI: 10.1590/s1415-475738420150025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 07/20/2015] [Indexed: 11/21/2022] Open
Abstract
The core microbiota of a neutral mine drainage and the surrounding high heavy metal content soil at a Brazilian copper mine were characterized by 16S rDNA pyrosequencing. The core microbiota of the drainage was dominated by the generalist genus Meiothermus. The soil samples contained a more heterogeneous bacterial community, with the presence of both generalist and specialist bacteria. Both environments supported mainly heterotrophic bacteria, including organisms resistant to heavy metals, although many of the bacterial groups identified remain poorly characterized. The results contribute to the understanding of bacterial communities in soils impacted by neutral mine drainage, for which information is scarce, and demonstrate that heavy metals can play an important role in shaping the microbial communities in mine environments.
Collapse
Affiliation(s)
- Letícia Bianca Pereira
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Renato Vicentini
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Laura M M Ottoboni
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| |
Collapse
|
23
|
Rao S, Chan Y, Bugler-Lacap DC, Bhatnagar A, Bhatnagar M, Pointing SB. Microbial Diversity in Soil, Sand Dune and Rock Substrates of the Thar Monsoon Desert, India. Indian J Microbiol 2015; 56:35-45. [PMID: 26843695 DOI: 10.1007/s12088-015-0549-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/14/2015] [Indexed: 11/24/2022] Open
Abstract
A culture-independent diversity assessment of archaea, bacteria and fungi in the Thar Desert in India was made. Six locations in Ajmer, Jaisalmer, Jaipur and Jodhupur included semi-arid soils, arid soils, arid sand dunes, plus arid cryptoendolithic substrates. A real-time quantitative PCR approach revealed that bacteria dominated soils and cryptoendoliths, whilst fungi dominated sand dunes. The archaea formed a minor component of all communities. Comparison of rRNA-defined community structure revealed that substrate and climate rather than location were the most parsimonious predictors. Sequence-based identification of 1240 phylotypes revealed that most taxa were common desert microorganisms. Semi-arid soils were dominated by actinobacteria and alpha proteobacteria, arid soils by chloroflexi and alpha proteobacteria, sand dunes by ascomycete fungi and cryptoendoliths by cyanobacteria. Climatic variables that best explained this distribution were mean annual rainfall and maximum annual temperature. Substrate variables that contributed most to observed diversity patterns were conductivity, soluble salts, Ca(2+) and pH. This represents an important addition to the inventory of desert microbiota, novel insight into the abiotic drivers of community assembly, and the first report of biodiversity in a monsoon desert system.
Collapse
Affiliation(s)
- Subramanya Rao
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology, Auckland, 1142 New Zealand
| | - Yuki Chan
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology, Auckland, 1142 New Zealand
| | - Donnabella C Bugler-Lacap
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology, Auckland, 1142 New Zealand
| | - Ashish Bhatnagar
- Department of Microbiology, Maharshi Dayanand Saraswathi University, Ajmer, Rajasthan India
| | - Monica Bhatnagar
- Department of Microbiology, Maharshi Dayanand Saraswathi University, Ajmer, Rajasthan India
| | - Stephen B Pointing
- Institute for Applied Ecology New Zealand, School of Applied Sciences, Auckland University of Technology, Auckland, 1142 New Zealand
| |
Collapse
|