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Manirakiza B, Zhang S, Addo FG, Yu M, Alklaf SA. Interactions between water quality and microbes in epiphytic biofilm and superficial sediment of lake in trophic agriculture area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169321. [PMID: 38103607 DOI: 10.1016/j.scitotenv.2023.169321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/05/2023] [Accepted: 12/10/2023] [Indexed: 12/19/2023]
Abstract
Epiphytic and superficial sediment biofilm-dwelling microbial communities play a pivotal role in water quality regulation and biogeochemical cycling in shallow lakes. However, the interactions are far from clear between water physicochemical parameters and microbial community on aquatic plants and in surface sediments of lake in trophic agriculture area. This study employed Illumina sequencing, Partial Least Squares Path Modeling (PLS-PM), and physico-chemical analytical methods to explore the interactions between water quality and microbes (bacteria and eukaryotes) in three substrates of trophic shallow Lake Cyohoha North, Rwanda. The Lake Cyohoha was significantly polluted with total phosphorus (TP), total nitrogen (TN), nitrate nitrogen (NO3-N), and ammonia nitrogen (NH3-N) in the wet season compared to the dry season. PLS-PM revealed a strong positive correlation (+0.9301) between land use types and physico-chemical variables in the rainy season. In three substrates of the trophic lake, Proteobacteria, Cyanobacteria, Firmicutes, and Actinobacteria were dominant phyla in the bacterial communities, and Rotifers, Platyhelminthes, Gastrotricha, and Ascomycota dominated in microeukaryotic communities. As revealed by null and neutral models, stochastic processes predominantly governed the assembly of bacterial and microeukaryotic communities in biofilms and surface sediments. Network analysis revealed that the microbial interconnections in Ceratophyllum demersum were more stable and complex compared to those in Eichhornia crassipes and sediments. Co-occurrence network analysis (|r| > 0.7, p < 0.05) revealed that there were complex interactions among physicochemical parameters and microbes in epiphytic and sediment biofilms, and many keystone microbes on three substrates played important role in nutrients removal, food web and microbial community stable. These findings emphasize that eutrophic water influence the structure, composition, and interactions of microbes in epiphytic and surface sediment biofilms, and provided new insights into the interconnections between water quality and microbial community in presentative substrates in tropical lacustrine ecosystems in agriculturally polluted areas. The study provides useful information for water quality protection and aquatic plants restoration for policy making and catchment management.
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Affiliation(s)
- Benjamin Manirakiza
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China; University of Rwanda (UR), College of Science and Technology (CST), Department of Biology, 3900, Kigali, Rwanda
| | - Songhe Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China.
| | - Felix Gyawu Addo
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Ma Yu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Salah Alden Alklaf
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
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2
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Power JF, Lowe CL, Carere CR, McDonald IR, Cary SC, Stott MB. Temporal dynamics of geothermal microbial communities in Aotearoa-New Zealand. Front Microbiol 2023; 14:1094311. [PMID: 37020721 PMCID: PMC10068964 DOI: 10.3389/fmicb.2023.1094311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/20/2023] [Indexed: 03/17/2023] Open
Abstract
Microbial biogeography studies, in particular for geothermal-associated habitats, have focused on spatial patterns and/or individual sites, which have limited ability to describe the dynamics of ecosystem behaviour. Here, we report the first comprehensive temporal study of bacterial and archaeal communities from an extensive range of geothermal features in Aotearoa-New Zealand. One hundred and fifteen water column samples from 31 geothermal ecosystems were taken over a 34-month period to ascertain microbial community stability (control sites), community response to both natural and anthropogenic disturbances in the local environment (disturbed sites) and temporal variation in spring diversity across different pH values (pH 3, 5, 7, 9) all at a similar temperature of 60–70°C (pH sites). Identical methodologies were employed to measure microbial diversity via 16S rRNA gene amplicon sequencing, along with 44 physicochemical parameters from each feature, to ensure confidence in comparing samples across timeframes. Our results indicated temperature and associated groundwater physicochemistry were the most likely parameters to vary stochastically in these geothermal features, with community abundances rather than composition more readily affected by a changing environment. However, variation in pH (pH ±1) had a more significant effect on community structure than temperature (±20°C), with alpha diversity failing to adequately measure temporal microbial disparity in geothermal features outside of circumneutral conditions. While a substantial physicochemical disturbance was required to shift community structures at the phylum level, geothermal ecosystems were resilient at this broad taxonomic rank and returned to a pre-disturbed state if environmental conditions re-established. These findings highlight the diverse controls between different microbial communities within the same habitat-type, expanding our understanding of temporal dynamics in extreme ecosystems.
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Affiliation(s)
- Jean F. Power
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
| | - Caitlin L. Lowe
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
| | - Carlo R. Carere
- Te Tari Pūhanga Tukanga Matū | Department of Chemical and Process Engineering, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, Aotearoa-New Zealand
| | - Ian R. McDonald
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
| | - S. Craig Cary
- Thermophile Research Unit, Te Aka Mātuatua | School of Science, Te Whare Wānanga o Waikato | University of Waikato, Hamilton, New Zealand
- S. Craig Cary,
| | - Matthew B. Stott
- Biomolecular Interaction Centre, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, Aotearoa-New Zealand
- Te Kura Pūtaiao Koiora | School of Biological Sciences, Te Whare Wānanga o Waitaha | University of Canterbury, Christchurch, New Zealand
- *Correspondence: Matthew B. Stott,
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Chen J, Liu H, Bai Y, Qi J, Qi W, Liu H, Peng J, Qu J. Mixing regime shapes the community assembly process, microbial interaction and proliferation of cyanobacterial species Planktothrix in a stratified lake. J Environ Sci (China) 2022; 115:103-113. [PMID: 34969441 DOI: 10.1016/j.jes.2021.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/04/2021] [Accepted: 07/05/2021] [Indexed: 06/14/2023]
Abstract
Lake mixing influences aquatic chemical properties and microbial community composition, and thus, we hypothesized that it would alter microbial community assembly and interaction. To clarify this issue, we explored the community assembly processes and cooccurrence networks in four seasons at two depths (epilimnion and hypolimnion) in a mesotrophic and stratified lake (Chenghai Lake), which formed stratification in the summer and turnover in the winter. During the stratification period, the epilimnion and hypolimnion went through contrary assembly processes but converged to similar assembly patterns in the mixing period. In a highly homogeneous selection environment, species with low niche breadth were filtered, resulting in decreased species richness. Water mixing in the winter homogenized the environment, resulting in a simpler microbial cooccurrence network. Interestingly, we observed a high abundance of the cyanobacterial genus Planktothrix in the winter, probably due to nutrient redistribution and Planktothrix adaptivity to the winter environment in which mixing played important roles. Our study provides deeper fundamental insights into how environmental factors influence microbial community structure through community assembly processes.
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Affiliation(s)
- Junwen Chen
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Huacong Liu
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yaohui Bai
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jing Qi
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weixiao Qi
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Huijuan Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jianfeng Peng
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiuhui Qu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China; Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
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Fonseca VG, Kirse A, Giebner H, Vause BJ, Drago T, Power DM, Peck LS, Clark MS. Metabarcoding the Antarctic Peninsula biodiversity using a multi-gene approach. ISME COMMUNICATIONS 2022; 2:37. [PMID: 37938273 PMCID: PMC9723778 DOI: 10.1038/s43705-022-00118-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 07/04/2023]
Abstract
Marine sediment communities are major contributors to biogeochemical cycling and benthic ecosystem functioning, but they are poorly described, particularly in remote regions such as Antarctica. We analysed patterns and drivers of diversity in metazoan and prokaryotic benthic communities of the Antarctic Peninsula with metabarcoding approaches. Our results show that the combined use of mitochondrial Cox1, and 16S and 18S rRNA gene regions recovered more phyla, from metazoan to non-metazoan groups, and allowed correlation of possible interactions between kingdoms. This higher level of detection revealed dominance by the arthropods and not nematodes in the Antarctic benthos and further eukaryotic diversity was dominated by benthic protists: the world's largest reservoir of marine diversity. The bacterial family Woeseiaceae was described for the first time in Antarctic sediments. Almost 50% of bacteria and 70% metazoan taxa were unique to each sampled site (high alpha diversity) and harboured unique features for local adaptation (niche-driven). The main abiotic drivers measured, shaping community structure were sediment organic matter, water content and mud. Biotic factors included the nematodes and the highly abundant bacterial fraction, placing protists as a possible bridge for between kingdom interactions. Meiofauna are proposed as sentinels for identifying anthropogenic-induced changes in Antarctic marine sediments.
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Affiliation(s)
- V G Fonseca
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, UK.
| | - A Kirse
- Zoological Research Museum Alexander Koenig (ZFMK), Bonn, Germany
| | - H Giebner
- Zoological Research Museum Alexander Koenig (ZFMK), Bonn, Germany
| | - B J Vause
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - T Drago
- Portuguese Institute for Sea and Atmosphere (IPMA), Tavira, Portugal
- Institute Dom Luiz (IDL), University of Lisbon, Lisbon, Portugal
| | - D M Power
- Centre of Marine Sciences (CCMAR), Faro, Portugal
| | - L S Peck
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
| | - M S Clark
- British Antarctic Survey, Natural Environment Research Council, Cambridge, UK
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Manirakiza B, Zhang S, Addo FG, Isabwe A, Nsabimana A. Exploring microbial diversity and ecological function of epiphytic and surface sediment biofilm communities in a shallow tropical lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 808:151821. [PMID: 34808175 DOI: 10.1016/j.scitotenv.2021.151821] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities in epiphytic biofilms and surface sediments play a vital role in the biogeochemical cycles of the major chemical elements in freshwater. However, little is known about the diversity, composition, and ecological functions of microbial communities in shallow tropical lakes dominated by aquatic macrophytes. In this study, epiphytic bacterial and eukaryotic biofilm communities on submerged and floating macrophytes and surface sediments were investigated in Lake Rumira, Rwanda in August and November 2019. High-throughput sequencing data revealed that members of the phyla, including Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria, Chloroflexi, Bacteriodetes, Verrumicrobia, and Myxomycota, dominated bacterial communities, while the microeukaryotic communities were dominated by Unclassified (uncl) SAR(Stramenopiles, Alveolata, Rhizaria), Rotifers, Ascomycota, Gastrotricha, Platyhelminthes, Chloroplastida, and Arthropoda. Interestingly, the eukaryotic OTUs (operational taxonomic units) number and Shannon indices were significantly higher in sediments and epiphytic biofilms on Eicchornia crassipes than Ceratophyllum demersum (p < 0.05), while no differences were observed in bacterial OTUs number and Shannon values among substrates. Redundancy analysis (RDA) showed that water temperature, pH, dissolved oxygen (DO), total nitrogen (TN), and electrical conductivity (EC) were the most important abiotic factors closely related to the microbial community on C. demersum and E. crassipes. Furthermore, co-occurrence networks analysis (|r| > 0.7, p < 0.05) and functional prediction revealed more complex interactions among microbes on C. demersum than on E. crassipes and sediments, and those interactions include cross-feeding, parasitism, symbiosis, and predatism among organisms in biofilms. These results suggested that substrate-type and environmental factors were the strong driving forces of microbial diversity in epiphytic biofilms and surface sediments, thus shedding new insights into microbial community diversity in epiphytic biofilms and surface sediments and its ecological role in tropical lacustrine ecosystems.
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Affiliation(s)
- Benjamin Manirakiza
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China; University of Rwanda (UR), College of Science and Technology (CST), Department of Biology, P.O. Box 3900, Kigali, Rwanda
| | - Songhe Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China.
| | - Felix Gyawu Addo
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Alain Isabwe
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Antoine Nsabimana
- University of Rwanda (UR), College of Science and Technology (CST), Department of Biology, P.O. Box 3900, Kigali, Rwanda
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6
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Mechanisms Driving Microbial Community Composition in Anaerobic Co-Digestion of Waste-Activated Sewage Sludge. Bioengineering (Basel) 2021; 8:bioengineering8120197. [PMID: 34940350 PMCID: PMC8699016 DOI: 10.3390/bioengineering8120197] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 11/17/2022] Open
Abstract
Anaerobic co-digestion (Co-AD) is used to increase the effectiveness of anaerobic digestion (AD) using local “wastes”, adding economic and environmental benefits. Since system stability is of existential importance for the operation of wastewater treatment plants, thorough testing of potential co-substrates and their effects on the respective community and system performance is crucial for understanding and utilizing Co-AD to its best capacity. Food waste (FW) and canola lecithin (CL) were tested in mesophilic, lab-scale, semi-continuous reactors over a duration of 120 days with stepwise increased substrate addition. Key performance indicators (biogas, total/volatile solids, fatty acids) were monitored and combined with 16S-rRNA amplicon sequencing to assess the impact of co-substrate addition on reactor performance and microbial community composition (MCC). Additionally, the latter was then compared with natural shifts occurring in the wastewater treatment plant (WWTP, source) at the same time. An almost linear increase in biogas production with both co-substrates at an approximate 1:1 ratio with the organic loading rate (OLR) was observed. The MCCs in both experiments were mostly stable, but also prone to drift over time. The FW experiment MCC more closely resembled the original WWTP community and the observed shifts indicated high levels of functional redundancy. Exclusive to the CL co-substrate, a clear selection for a few operational taxonomic units (OTUs) was observed. There was little evidence for a persistent invasion and establishment of microorganisms from typical primary substrates into the stable resident community of the reactors, which is in line with earlier findings that suggested that the inoculum and history mostly define the MCC. However, external factors may still tip the scales in favor of a few r-strategists (e.g., Prolixibacter) in an environment that otherwise favors K-strategists, which may in fact also be recruited from the primary substrate (Trichococcus). In our study, specialization and diversity loss were also observed in response to the addition of the highly specialized CL, which in turn, may have adverse effects on the system’s stability and reduced resilience and recovery.
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David GM, López-García P, Moreira D, Alric B, Deschamps P, Bertolino P, Restoux G, Rochelle-Newall E, Thébault E, Simon M, Jardillier L. Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns. Mol Ecol 2021; 30:2162-2177. [PMID: 33639035 DOI: 10.1111/mec.15864] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/27/2022]
Abstract
Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water quality. Because of their small size, these ecosystems are in principle more sensitive to disturbances, seasonal variation and pluri-annual climate change. However, how microbial community composition varies over space and time, and whether archaeal, bacterial and microbial eukaryote communities behave similarly remain unanswered. Here, we aim to unravel the composition and intra/interannual temporal dynamic patterns for archaea, bacteria and microbial eukaryotes in a set of small freshwater ecosystems. We monitored archaeal and bacterial community composition during 24 consecutive months in four ponds and one brook from northwestern France by 16S rRNA gene amplicon sequencing (microbial eukaryotes were previously investigated for the same systems). Unexpectedly for oxic environments, bacterial Candidate Phyla Radiation (CPR) were highly diverse and locally abundant. Our results suggest that microbial community structure is mainly driven by environmental conditions acting over space (ecosystems) and time (seasons). A low proportion of operational taxonomic units (OTUs) (<1%) was shared by the five ecosystems despite their geographical proximity (2-9 km away), making microbial communities almost unique in each ecosystem and highlighting the strong selective influence of local environmental conditions. Marked and similar seasonality patterns were observed for archaea, bacteria and microbial eukaryotes in all ecosystems despite strong turnovers of rare OTUs. Over the 2-year survey, microbial community composition varied despite relatively stable environmental parameters. This suggests that biotic associations play an important role in interannual community assembly.
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Affiliation(s)
- Gwendoline M David
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | | | - David Moreira
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Benjamin Alric
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, Villeurbanne, France
| | - Philippe Deschamps
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Paola Bertolino
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Gwendal Restoux
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Emma Rochelle-Newall
- Sorbonne Université, UPEC, CNRS, IRD, INRAE, Institute d'Ecologie de des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
| | - Elisa Thébault
- Sorbonne Université, UPEC, CNRS, IRD, INRAE, Institute d'Ecologie de des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
| | - Marianne Simon
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Ludwig Jardillier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
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Vass M, Székely AJ, Lindström ES, Osman OA, Langenheder S. Warming mediates the resistance of aquatic bacteria to invasion during community coalescence. Mol Ecol 2021; 30:1345-1356. [PMID: 33448073 DOI: 10.1111/mec.15800] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 01/04/2023]
Abstract
The immigration history of communities can profoundly affect community composition. For instance, early-arriving species can have a lasting effect on community structure by reducing the invasion success of late-arriving ones through priority effects. This can be particularly important when early-arriving communities coalesce with another community during dispersal (mixing) events. However, the outcome of such community coalescence is unknown as we lack knowledge on how different factors influence the persistence of early-arriving communities and the invasion success of late-arriving taxa. Therefore, we implemented a full-factorial experiment with aquatic bacteria where temperature and dispersal rate of a better adapted community were manipulated to test their joint effects on the resistance of early-arriving communities to invasion, both at community and population level. Our 16S rRNA gene sequencing-based results showed that invasion success of better adapted late-arriving bacteria equaled or even exceeded what we expected based on the dispersal ratios of the recipient and invading communities suggesting limited priority effects on the community level. Patterns detected at the population level, however, showed that resistance of aquatic bacteria to invasion might be strengthened by warming as higher temperatures (a) increased the sum of relative abundances of persistent bacteria in the recipient communities, and (b) restricted the total relative abundance of successfully established late-arriving bacteria. Warming-enhanced resistance, however, was not always found and its strengths differed between recipient communities and dispersal rates. Nevertheless, our findings highlight the potential role of warming in mitigating the effects of invasion at the population level.
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Affiliation(s)
- Máté Vass
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
| | - Anna J Székely
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
| | - Eva S Lindström
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
| | - Omneya A Osman
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
| | - Silke Langenheder
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
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9
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Li L, Ma ZS. Species Sorting and Neutral Theory Analyses Reveal Archaeal and Bacterial Communities Are Assembled Differently in Hot Springs. Front Bioeng Biotechnol 2020; 8:464. [PMID: 32548097 PMCID: PMC7271673 DOI: 10.3389/fbioe.2020.00464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 04/21/2020] [Indexed: 12/03/2022] Open
Abstract
Although the recognition of archaea as one of the three kingdoms in the tree of life has been nearly a half-century long, the comparative investigations on their ecological adaptations with bacteria have been limited. The mechanisms of their community assembly and diversity maintenance in hot springs have not been addressed. The mechanistic study is critical not only for understanding the hot-spring microbiome structure and dynamics, but also for shedding light on their evolutionary adaptations. We applied the neutral theory model and species sorting paradigm of metacommunity theory to investigate how hot-spring microbial communities were assembled, how their diversities were maintained, and how the temperature and pH influence these mechanisms. Through rigorous statistical tests based on the neutral theory and species sorting paradigm, we found (i) According to the neutral theory, archaeal and bacterial communities are assembled differently, with stochastic neutral force playing a more significant role in archaeal communities than in bacterial communities (neutrality-rate = 52.9 vs. 15.8%, p-value < 0.05). (ii) Temperature and pH account for rather limited (<10%) variations in hot-spring microbiomes based on the species sorting paradigm. The pH has more significant influences than temperature on archaeal communities, and both pH and temperature have similarly low influences on bacterial community structure. (iii) We postulate that the differences between archaea and bacteria are likely due to the longer evolutionary history and better adaptation of archaea to host spring environments.
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Affiliation(s)
- Lianwei Li
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Zhanshan Sam Ma
- Computational Biology and Medical Ecology Lab, State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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10
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Variability in the Response of Bacterial Community Assembly to Environmental Selection and Biotic Factors Depends on the Immigrated Bacteria, as Revealed by a Soil Microcosm Experiment. mSystems 2019; 4:4/6/e00496-19. [PMID: 31796565 PMCID: PMC6890929 DOI: 10.1128/msystems.00496-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The soil microbiota conducts important biological ecosystem functions, but the mechanism underlying community-environment interactions for soil microbiota remains unclear. By using two distinct soils for cross inoculation, we successfully simulated the assembly of the bacterial community in sterile soil. Thus, the reasons why inoculum and recipient have dominated community assembly in previous investigations are investigated in this study. We found that inoculated bacteria presided over environmental selection for community assembly due to the varied difference of ecological equivalent bacteria, either divergent or convergent. The significance of neutrality for the ecologically equivalent bacterial species that immigrated into the recipients should be emphasized in exploring the mechanisms of community assembly. Our finding is helpful for understanding the community-environment interaction, a basic question in ecology, and it would shed light on this issue that has perplexed scientists for many years. Exploring the assembly mechanism of microbiota is critical for understanding soil ecosystem functions. However, the relative importance of different biotic and abiotic factors in determining the bacterial community has not been properly clarified. In this study, the effects of inocula and recipients on the assembly of the soil community were investigated to evaluate their importance by inoculation experiments with sterile soil. Two distinct soils, conventional nitrogen-fertilized soil and aromatic-compound-contaminated soil, were sterilized, cross inoculated, and incubated for 2 months under different inoculation doses and oxygen conditions. The results showed that the greatest variation in community structure emerged in the samples inoculated with distinct inocula rather than in the samples of different soil recipients. The phylogenies in the two inocula were diverse and dissimilar, although there were many ecologically equivalent bacteria. When the inocula with dissimilar ecologically equivalent species were used, the assembled communities were primarily determined by the inocula as indicated by the beta diversity and variation partitioning analyses. In contrast, environmental selection dominated the process when ecologically equivalent species in the inocula were similar, as when only one type of inoculum was used, where the soil habitat selected the most adaptive bacteria from the defined inoculum pool. These results indicate that inoculated bacteria are dominant over environmental selection if they are sufficiently dissimilar, although the effect of environmental selection is more obvious when similar bacteria are inoculated in the soil for community assembly. Our findings suggest that the immigration of exotic bacteria could be a primary factor impacting community assembly. IMPORTANCE The soil microbiota conducts important biological ecosystem functions, but the mechanism underlying community-environment interactions for soil microbiota remains unclear. By using two distinct soils for cross inoculation, we successfully simulated the assembly of the bacterial community in sterile soil. Thus, the reasons why inoculum and recipient have dominated community assembly in previous investigations are investigated in this study. We found that inoculated bacteria presided over environmental selection for community assembly due to the varied difference of ecological equivalent bacteria, either divergent or convergent. The significance of neutrality for the ecologically equivalent bacterial species that immigrated into the recipients should be emphasized in exploring the mechanisms of community assembly. Our finding is helpful for understanding the community-environment interaction, a basic question in ecology, and it would shed light on this issue that has perplexed scientists for many years.
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11
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Zheng W, Wen X. How exogenous influent communities and environmental conditions affect activated sludge communities in the membrane bioreactor of a wastewater treatment plant. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 692:622-630. [PMID: 31539970 DOI: 10.1016/j.scitotenv.2019.07.310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 07/19/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
In this study, the residual population of influent and activated sludge (AS) communities was defined based on their occurrence frequency and relative abundance through long-term and fine-scale sampling from the membrane bioreactor (MBR) of a wastewater treatment plant (WWTP). There were 481 OTUs defined as the residual OTUs, which taken up 67.90 ± 9.36% of relative abundance in the influent community. Besides, 6.76 ± 5.71% of the residual population migrated to and remained in the AS community. Additionally, the residual populations were more likely to be anaerobes and microaerobes. As the most predominant genus from residual community, the relative abundance of Arcobacter was reduced from 15.78 ± 3.58% in the influent to 1.15 ± 1.35% in the AS. The residues that migrated from the influent have increased the richness and evenness of AS community, as well as the dissimilarities among samples over long-term. The rank-abundance distribution showed identical pattern for the residual species between influent and AS. By adopting the analysis of neutral model, 2766 out of 7491 shared OTUs between influent and AS communities were identified as neutral OTUs, which respectively made up 53.9% and 41.8% of the total relative abundance of influent and AS communities. These indicated that the AS community was to some extent, but not entirely assembled by neutral process. For the residual community in the AS, dissolved oxygen (DO) was positively associated with several aerobic genera, meanwhile influent chemical oxygen demand (COD) had positive relationship with genus Pseudomonas. Last but most importantly, the influent community could not inoculate the nitrifiers in the AS, but instead, was able to inoculate the denitrifiers; as well as enhance the biodiversity and the ability of resisting external disturbance for the AS community in MBR.
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Affiliation(s)
- Wanlin Zheng
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China
| | - Xianghua Wen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, PR China.
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12
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Wilber MQ, Jani AJ, Mihaljevic JR, Briggs CJ. Fungal infection alters the selection, dispersal and drift processes structuring the amphibian skin microbiome. Ecol Lett 2019; 23:88-98. [PMID: 31637835 DOI: 10.1111/ele.13414] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/17/2019] [Accepted: 09/29/2019] [Indexed: 12/23/2022]
Abstract
Symbiotic microbial communities are important for host health, but the processes shaping these communities are poorly understood. Understanding how community assembly processes jointly affect microbial community composition is limited because inflexible community models rely on rejecting dispersal and drift before considering selection. We developed a flexible community assembly model based on neutral theory to ask: How do dispersal, drift and selection concurrently affect the microbiome across environmental gradients? We applied this approach to examine how a fungal pathogen affected the assembly processes structuring the amphibian skin microbiome. We found that the rejection of neutrality for the amphibian microbiome across a fungal gradient was not strictly due to selection processes, but was also a result of species-specific changes in dispersal and drift. Our modelling framework brings the qualitative recognition that niche and neutral processes jointly structure microbiomes into quantitative focus, allowing for improved predictions of microbial community turnover across environmental gradients.
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Affiliation(s)
- Mark Q Wilber
- Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Andrea J Jani
- Department of Oceanography, University of Hawai'i at Manoa, Honolulu, HI, 96822, USA
| | - Joseph R Mihaljevic
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Cheryl J Briggs
- Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, 93106, USA
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13
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Kavazos CRJ, Huggett MJ, Mueller U, Horwitz P. Bacterial and ciliate biofilm community structure at different spatial levels of a salt lake meta-community. FEMS Microbiol Ecol 2019; 94:5066167. [PMID: 30124812 DOI: 10.1093/femsec/fiy148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 08/01/2018] [Indexed: 11/14/2022] Open
Abstract
Meta-communities are assembled along an ecological scale that determines local and regional diversity. Spatial patterns have been detected in planktonic bacterial communities at distances <20 m, but little is known about the occurrence of similar variation for other microbial groups and changes in microbial meta-community assembly at different levels of a meta-community. To examine this variation, the biofilm of eight saline ponds were used to investigate processes shaping diversity within ponds (β) and between ponds (δ). Bacterial and ciliate communities were assessed using ARISA and T-RFLP respectively, while diversity partitioning methods were used to examine the importance of taxonomic turnover and variation partitioning was used to distinguish spatial from environmental determinants. The results show that turnover is important for determining β- and δ-diversity of biofilms. Spatial factors are important drivers of bacterial β-diversity but were unimportant for ciliate β-diversity. Environmental variation was a strong determinant of bacterial and ciliate δ-diversity, suggesting sorting processes are important for assembling pond communities. Determinants of diversity in bacteria are not universal for ciliates, suggesting higher functional redundancy of bacteria or the greater niche breadth of ciliates may be important in discriminating assembly processes between the two organisms.
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Affiliation(s)
- Christopher R J Kavazos
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Megan J Huggett
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia.,School of Environmental and Life Sciences, The University of Newcastle, 10 Chittaway Dr, Ourimbah, NSW 2258, Australia
| | - Ute Mueller
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia.,Centre for Marine Ecosystems Research, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
| | - Pierre Horwitz
- Centre for Ecosystem Management, School of Science, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA 6027, Australia
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14
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Sieber M, Pita L, Weiland-Bräuer N, Dirksen P, Wang J, Mortzfeld B, Franzenburg S, Schmitz RA, Baines JF, Fraune S, Hentschel U, Schulenburg H, Bosch TCG, Traulsen A. Neutrality in the Metaorganism. PLoS Biol 2019; 17:e3000298. [PMID: 31216282 PMCID: PMC6583948 DOI: 10.1371/journal.pbio.3000298] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 05/15/2019] [Indexed: 02/07/2023] Open
Abstract
Almost all animals and plants are inhabited by diverse communities of microorganisms, the microbiota, thereby forming an integrated entity, the metaorganism. Natural selection should favor hosts that shape the community composition of these microbes to promote a beneficial host-microbe symbiosis. Indeed, animal hosts often pose selective environments, which only a subset of the environmentally available microbes are able to colonize. How these microbes assemble after colonization to form the complex microbiota is less clear. Neutral models are based on the assumption that the alternatives in microbiota community composition are selectively equivalent and thus entirely shaped by random population dynamics and dispersal. Here, we use the neutral model as a null hypothesis to assess microbiata composition in host organisms, which does not rely on invoking any adaptive processes underlying microbial community assembly. We show that the overall microbiota community structure from a wide range of host organisms, in particular including previously understudied invertebrates, is in many cases consistent with neutral expectations. Our approach allows to identify individual microbes that are deviating from the neutral expectation and are therefore interesting candidates for further study. Moreover, using simulated communities, we demonstrate that transient community states may play a role in the deviations from the neutral expectation. Our findings highlight that the consideration of neutral processes and temporal changes in community composition are critical for an in-depth understanding of microbiota-host interactions.
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Affiliation(s)
- Michael Sieber
- Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Lucía Pita
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
| | | | - Philipp Dirksen
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Zoological Institute, University of Kiel, Kiel, Germany
| | - Jun Wang
- Institute of Microbiology, Chinese Academy of Science, Beijing, China
| | | | - Sören Franzenburg
- Institute for Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Ruth A. Schmitz
- Institute for General Microbiology, University of Kiel, Kiel, Germany
| | - John F. Baines
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Institute for Experimental Medicine, University of Kiel, Kiel, Germany
| | | | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research, Kiel, Germany
- Zoological Institute, University of Kiel, Kiel, Germany
| | - Hinrich Schulenburg
- Max Planck Institute for Evolutionary Biology, Plön, Germany
- Zoological Institute, University of Kiel, Kiel, Germany
| | | | - Arne Traulsen
- Max Planck Institute for Evolutionary Biology, Plön, Germany
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15
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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.
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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
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16
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Experimental Evidence that Stochasticity Contributes to Bacterial Composition and Functioning in a Decomposer Community. mBio 2019; 10:mBio.00568-19. [PMID: 30992354 PMCID: PMC6469972 DOI: 10.1128/mbio.00568-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Randomness can alter the diversity and composition of ecological communities. Such stochasticity may therefore obscure the relationship between the environment and community composition and hinder our ability to predict the relationship between biodiversity and ecosystem functioning. This study investigated the role of stochastic processes, environmental selection, and dispersal in microbial composition and its functioning on an intact field community. To do this, we used a controlled and replicated experiment that was similar to that used to study population genetics in the laboratory. Our study showed that, while the stochastic effects on taxonomic composition are smaller than expected, the degree to which stochasticity contributes to variability in ecosystem processes may be much higher than previously assumed. Stochasticity emerging from random differences in replication, death, mutation, and dispersal is thought to alter the composition of ecological communities. However, the importance of stochastic effects remains somewhat speculative because stochasticity is not directly measured but is instead inferred from unexplained variations in beta-diversity. Here, we performed a field experiment to more directly disentangle the role of stochastic processes, environmental selection, and dispersal in the composition and functioning of a natural bacterial decomposer community in the field. To increase our ability to detect these effects, we reduced initial biological and environmental heterogeneity using replicate nylon litterbags in the field. We then applied two treatments: ambient/added precipitation and bacterial and fungal dispersal using “open” litterbags (made from 18.0-μm-pore-size mesh) (“open bacterial dispersal”) versus bacterial and fungal dispersal using “closed” litterbags (made from 22.0-μm-pore-size mesh) (“closed bacterial dispersal”). After 5 months, we assayed composition and functioning by the use of three subsamples from each litterbag to disentangle stochastic effects from residual variation. Our results indicate that stochasticity via ecological drift can contribute to beta-diversity in bacterial communities. However, residual variation, which had previously been included in stochasticity estimates, accounted for more than four times as much variability. At the same time, stochastic effects on beta-diversity were not attenuated at the functional level, as measured by genetic functional potential and extracellular enzyme activity. Finally, dispersal was found to interact with precipitation availability to influence the degree to which stochasticity contributed to functional variation. Together, our results demonstrate that the ability to quantify stochastic processes is key to understanding microbial diversity and its role in ecosystem functioning.
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17
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Frequency of disturbance alters diversity, function, and underlying assembly mechanisms of complex bacterial communities. NPJ Biofilms Microbiomes 2019; 5:8. [PMID: 30774969 PMCID: PMC6370796 DOI: 10.1038/s41522-019-0079-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 12/11/2018] [Indexed: 01/10/2023] Open
Abstract
Disturbance is known to affect the ecosystem structure, but predicting its outcomes remains elusive. Similarly, community diversity is believed to relate to ecosystem functions, yet the underlying mechanisms are poorly understood. Here, we tested the effect of disturbance on the structure, assembly, and ecosystem function of complex microbial communities within an engineered system. We carried out a microcosm experiment where activated sludge bioreactors operated in daily cycles were subjected to eight different frequency levels of augmentation with a toxic pollutant, from never (undisturbed) to every day (press-disturbed), for 35 days. Microbial communities were assessed by combining distance-based methods, general linear multivariate models, α-diversity indices, and null model analyses on metagenomics and 16S rRNA gene amplicon data. A stronger temporal decrease in α-diversity at the extreme, undisturbed and press-disturbed, ends of the disturbance range led to a hump-backed pattern, with the highest diversity found at intermediate levels of disturbance. Undisturbed and press-disturbed levels displayed the highest community and functional similarity across replicates, suggesting deterministic processes were dominating. The opposite was observed amongst intermediately disturbed levels, indicating stronger stochastic assembly mechanisms. Trade-offs were observed in the ecosystem function between organic carbon removal and both nitrification and biomass productivity, as well as between diversity and these functions. Hence, not every ecosystem function was favoured by higher community diversity. Our results show that the assessment of changes in diversity, along with the underlying stochastic–deterministic assembly processes, is essential to understanding the impact of disturbance in complex microbial communities. Complex microbial communities and ecosystems are highly sensitive to disturbance, which can affect community diversity and structure, but to date the impact of disturbance remains difficult to predict. Here, Stefan Wuertz and colleagues from the Nanyang Technological University in Singapore show how different disturbance frequencies affect microbial population dynamics. Analyses of microbial communities in sludge bioreactors exposed to a toxic pollutant at different rates revealed that populations at the extremes (not exposed and most exposed) showed the lowest α-diversity, whereas populations exposed at intermediate levels were most diverse. Notably, ecosystem function trade-offs were observed between organic carbon removal and nitrification and biomass productivity, with diversity also affecting these functions. These observations highlight the importance of evaluating diversity when determining the effects of disturbance on microbial communities.
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18
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Multiple processes acting from local to large geographical scales shape bacterial communities associated with Phormidium (cyanobacteria) biofilms in French and New Zealand rivers. Sci Rep 2018; 8:14416. [PMID: 30258224 PMCID: PMC6158260 DOI: 10.1038/s41598-018-32772-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 09/12/2018] [Indexed: 11/08/2022] Open
Abstract
River biofilms dominated by Phormidium (cyanobacteria) are receiving increased attention worldwide because of a recent expansion in their distribution and their ability to produce neurotoxins leading to animal mortalities. Limited data are available on the composition and structure of bacterial communities (BCs) associated with Phormidium biofilms despite the important role they potentially play in biofilm functioning. By using a high-throughput sequencing approach, we compared the BCs associated with Phormidium biofilms in several sampling sites of the Tarn River (France) and in eight New Zealand rivers. The structure of the BCs from both countries displayed spatial and temporal variations but were well conserved at the order level and 28% of the OTUs containing 90% of the reads were shared by these BCs. This suggests that micro-environmental conditions occurring within thick Phormidium biofilms strongly shape the associated BCs. A strong and significant distance-decay relationship (rp = 0.7; P = 0.001) was found in BCs from New Zealand rivers but the Bray-Curtis dissimilarities between French and New Zealand BCs are in the same order of magnitude of those found between New Zealand BCs. All these findings suggest that local environmental conditions seem to have more impact on BCs than dispersal capacities of bacteria.
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19
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Ruiz-González C, Archambault E, Laforest-Lapointe I, del Giorgio PA, Kembel SW, Messier C, Nock CA, Beisner BE. Soils associated to different tree communities do not elicit predictable responses in lake bacterial community structure and function. FEMS Microbiol Ecol 2018; 94:5037915. [DOI: 10.1093/femsec/fiy115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 06/14/2018] [Indexed: 01/09/2023] Open
Affiliation(s)
- Clara Ruiz-González
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
- Department of Biological Sciences, University of Québec at Montréal, Montréal, Canada
| | - Esther Archambault
- Department of Biological Sciences, University of Québec at Montréal, Montréal, Canada
| | | | - Paul A del Giorgio
- Department of Biological Sciences, University of Québec at Montréal, Montréal, Canada
| | - Steven W Kembel
- Department of Biological Sciences, University of Québec at Montréal, Montréal, Canada
| | - Christian Messier
- Department of Biological Sciences, University of Québec at Montréal, Montréal, Canada
| | - Charles A Nock
- Geobotany, Faculty of Biology, University of Freiburg, Germany
| | - Beatrix E Beisner
- Department of Biological Sciences, University of Québec at Montréal, Montréal, Canada
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20
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Liu J, Li C, Jing J, Zhao P, Luo Z, Cao M, Ma Z, Jia T, Chai B. Ecological patterns and adaptability of bacterial communities in alkaline copper mine drainage. WATER RESEARCH 2018; 133:99-109. [PMID: 29367051 DOI: 10.1016/j.watres.2018.01.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 12/31/2017] [Accepted: 01/05/2018] [Indexed: 06/07/2023]
Abstract
Environmental gradient have strong effects on community assembly processes. In order to reveal the effects of alkaline mine drainage (AlkMD) on bacterial and denitrifying bacterial community compositions and diversity in tailings reservoir, here we conducted an experiment to examine all and core bacterial taxa and denitrifying functional genes's (nirS, nirK, nosZΙ) abundance along a chemical gradient in tailings water in Shibahe copper tailings in Zhongtiaoshan, China. Differences in bacterial and denitrifying bacterial community compositions in different habitats and their relationships with environmental parameters were analyzed. The results showed that the richness and diversity of bacterial community in downstream seeping water (SDSW) were the largest, while that in upstream tailings water (STW1) were the lowest. The diversity and abundance of bacterial communities tended to increase from STW1 to SDSW. The variation of bacterial community diversity was significantly related to electroconductibility (EC), nitrate (NO3-), nitrite (NO2-), total carbon (TC), inorganic carbon (IC) and sulfate (SO42-), but was not correlated with geographic distance in local scale. Core taxa from class to genus were all significantly related to NO3- and NO2-. Core taxa Rhodobacteraceae, Rhodobacter, Acinetobacter and Hydrogenophaga were typical denitrifying bacteria. The variation trends of these groups were consistent with the copy number of nirS, nirK and nosZΙ, demonstrating their importance in the process of nitrogen reduction. The copy number of nirK, nosZΙ and nirS/16S rDNA, nirK/16Sr DNA correlated strongly with NO3-, NO2- and IC, but nirS and nosZI/16SrDNA had no significant correlation with NO3- and NO2-. The copy numbers of denitrifying functional genes (nirS, nirK and nosZΙ) were negatively correlated with heavy metal plumbum (Pb) and zinc (Zn). It showed that heavy metal contamination was an important factor affecting the structure of denitrifying bacterial community in AlkMD. In this study we have identified the distribution pattern of bacterial community along physiochemical gradients in alkaline tailings reservoir and displayed the driving force of shaping the structure of bacterial community. The influence of NO3-, NO2-, IC and heavy metal Pb and Zn on bacterial community might via their influence on the functional groups involving nitrogen, carbon and metal metabolisms.
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Affiliation(s)
- Jinxian Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Cui Li
- Faculty of Environment Economics, Shanxi University of Finance and Economics, Taiyuan, 030006, China
| | - Juhui Jing
- Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Pengyu Zhao
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Zhengming Luo
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Miaowen Cao
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Zhuanzhuan Ma
- Institute of Biotechnology, Shanxi University, Taiyuan, 030006, China
| | - Tong Jia
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China
| | - Baofeng Chai
- Institute of Loess Plateau, Shanxi University, Taiyuan, 030006, China.
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21
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Kinnunen M, Gülay A, Albrechtsen HJ, Dechesne A, Smets BF. Nitrotogais selected overNitrospirain newly assembled biofilm communities from a tap water source community at increased nitrite loading. Environ Microbiol 2017; 19:2785-2793. [DOI: 10.1111/1462-2920.13792] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 05/02/2017] [Accepted: 05/02/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Marta Kinnunen
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet 115, 2800 Kgs Lyngby Denmark
| | - Arda Gülay
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet 115, 2800 Kgs Lyngby Denmark
| | - Hans-Jørgen Albrechtsen
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet 115, 2800 Kgs Lyngby Denmark
| | - Arnaud Dechesne
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet 115, 2800 Kgs Lyngby Denmark
| | - Barth F. Smets
- Department of Environmental Engineering; Technical University of Denmark; Bygningstorvet 115, 2800 Kgs Lyngby Denmark
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22
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Ruiz-González C, Niño-García JP, Kembel SW, Del Giorgio PA. Identifying the core seed bank of a complex boreal bacterial metacommunity. ISME JOURNAL 2017; 11:2012-2021. [PMID: 28585940 DOI: 10.1038/ismej.2017.67] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 02/20/2017] [Accepted: 04/07/2017] [Indexed: 11/09/2022]
Abstract
Seed banks are believed to contribute to compositional changes within and across microbial assemblages, but the application of this concept to natural communities remains challenging. Here we describe the core seed bank of a bacterial metacommunity from a boreal watershed, using the spatial distribution of bacterial operational taxonomic units (OTUs) across 223 heterogeneous terrestrial, aquatic and phyllosphere bacterial assemblages. Taxa were considered potential seeds if they transitioned from rare to abundant somewhere within the metacommunity and if they were ubiquitous and able to persist under unfavorable conditions, the latter assessed by checking their presence in three deeply sequenced samples (one soil, one river and one lake, 2.2-3 million reads per sample). We show that only a small fraction (13%) of all detected OTUs constitute a metacommunity seed bank that is shared between all terrestrial and aquatic communities, but not by phyllosphere assemblages, which seem to recruit from a different taxa pool. Our results suggest directional recruitment driven by the flow of water in the landscape, since most aquatic sequences were associated to OTUs found in a single deeply-sequenced soil sample, but only 45% of terrestrial sequences belonged to OTUs found in the two deeply-sequenced aquatic communities. Finally, we hypothesize that extreme rarity, and its interplay with water residence time and growth rates, may further constrain the size of the potential seed bank.
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Affiliation(s)
- Clara Ruiz-González
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Succursale Centre-Ville, Montréal, Quebec, Canada.,Institut de Ciències del Mar (ICM-CSIC), Departament de Biologia Marina i Oceanografia, Barcelona, Spain
| | - Juan Pablo Niño-García
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Succursale Centre-Ville, Montréal, Quebec, Canada.,Escuela de Microbiología, Universidad de Antioquia, Medellín, Colombia
| | - Steven W Kembel
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Succursale Centre-Ville, Montréal, Quebec, Canada
| | - Paul A Del Giorgio
- Groupe de Recherche Interuniversitaire en Limnologie et en Environnement Aquatique (GRIL), Département des Sciences Biologiques, Université du Québec à Montréal, Succursale Centre-Ville, Montréal, Quebec, Canada
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23
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Janzen T, Alzate A, Muschick M, Maan ME, van der Plas F, Etienne RS. Community assembly in Lake Tanganyika cichlid fish: quantifying the contributions of both niche-based and neutral processes. Ecol Evol 2017; 7:1057-1067. [PMID: 28303177 PMCID: PMC5306054 DOI: 10.1002/ece3.2689] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/07/2016] [Accepted: 11/27/2016] [Indexed: 02/03/2023] Open
Abstract
The cichlid family features some of the most spectacular examples of adaptive radiation. Evolutionary studies have highlighted the importance of both trophic adaptation and sexual selection in cichlid speciation. However, it is poorly understood what processes drive the composition and diversity of local cichlid species assemblages on relatively short, ecological timescales. Here, we investigate the relative importance of niche-based and neutral processes in determining the composition and diversity of cichlid communities inhabiting various environmental conditions in the littoral zone of Lake Tanganyika, Zambia. We collected data on cichlid abundance, morphometrics, and local environments. We analyzed relationships between mean trait values, community composition, and environmental variation, and used a recently developed modeling technique (STEPCAM) to estimate the contributions of niche-based and neutral processes to community assembly. Contrary to our expectations, our results show that stochastic processes, and not niche-based processes, were responsible for the majority of cichlid community assembly. We also found that the relative importance of niche-based and neutral processes was constant across environments. However, we found significant relationships between environmental variation, community trait means, and community composition. These relationships were caused by niche-based processes, as they disappeared in simulated, purely neutrally assembled communities. Importantly, these results can potentially reconcile seemingly contrasting findings in the literature about the importance of either niche-based or neutral-based processes in community assembly, as we show that significant trait relationships can already be found in nearly (but not completely) neutrally assembled communities; that is, even a small deviation from neutrality can have major effects on community patterns.
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Affiliation(s)
- Thijs Janzen
- Department of Evolutionary TheoryMax Planck Institute for Evolutionary BiologyPlönGermany
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Adriana Alzate
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
- Terrestrial Ecology UnitUniversity of GhentGhentBelgium
- Fundacion EcomaresCaliColombia
| | - Moritz Muschick
- Zoological InstituteUniversity of BaselBaselSwitzerland
- Department of Fish Ecology & EvolutionEAWAG Centre for EcologyKastanienbaumSwitzerland
| | - Martine E. Maan
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Fons van der Plas
- Institute of Plant SciencesUniversity of BernBernSwitzerland
- Biodiversity and Climate Research CentreSenckenberg Gesellschaft für NaturforschungFrankfurtGermany
| | - Rampal S. Etienne
- Groningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
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24
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Tao Y, Dai T, Huang B, Wen D. The impact of wastewater treatment effluent on microbial biomasses and diversities in coastal sediment microcosms of Hangzhou Bay. MARINE POLLUTION BULLETIN 2017; 114:355-363. [PMID: 27707472 DOI: 10.1016/j.marpolbul.2016.09.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 09/18/2016] [Accepted: 09/21/2016] [Indexed: 06/06/2023]
Abstract
Disposal of wastewater treatment plant (WWTP) effluent into sea, a typical anthropogenic disturbance, may influence many environmental factors and change the coastal microbial community structure. In this study, by setting up coastal sediment microcosms perturbed by WWTP effluent, the changes of microbial community structure under different degree of disturbances were investigated. Quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (T-RFLP) were used to analyzed the biomass and biodiversity. High throughput sequencing analysis was used to identify the classification of the microorganisms. Our study suggested that low ratio of WWTP effluent may stimulate dominant species, which increase the biomass but decrease the biodiversity; while high ratio of WWTP effluent may depress all species, which decrease the biomass but increase the biodiversity. In other words, the impact was dose-dependent. The changes of microbial community structure may provide a metric for water environmental assessment and pollution control.
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Affiliation(s)
- Yile Tao
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Tianjiao Dai
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China
| | - Bei Huang
- Zhejiang Provincial Zhoushan Marine Ecological Environmental Monitoring Station, Zhoushan 316021, China
| | - Donghui Wen
- College of Environmental Sciences and Engineering, The Key Laboratory of Water and Sediment Sciences (Ministry of Education), Peking University, Beijing 100871, China.
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25
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Adair KL, Douglas AE. Making a microbiome: the many determinants of host-associated microbial community composition. Curr Opin Microbiol 2016; 35:23-29. [PMID: 27907842 DOI: 10.1016/j.mib.2016.11.002] [Citation(s) in RCA: 147] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/07/2016] [Accepted: 11/14/2016] [Indexed: 02/07/2023]
Abstract
The composition of many host-associated microbial communities is characterized by seemingly contradictory features: strong selection for specific taxa by the host, but substantial variability among hosts and over time within one host. Recent advances have revealed that both deterministic and stochastic processes operating across multiple spatial scales shape the composition of host-associated microbial communities. Although most research has focused on deterministic processes within individual hosts, the microbiota within each host is increasingly recognized to contribute to a wider metacommunity maintained by transmission between individual hosts and dispersal between host-associated and free-living microbial communities. By applying a community ecology perspective encompassing the microbial metacommunity, the many determinants of host-associated microbial community composition can be identified, guiding the directions of future research.
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Affiliation(s)
- Karen L Adair
- Department of Entomology, Cornell University, Ithaca 14853, NY, USA
| | - Angela E Douglas
- Department of Entomology, Cornell University, Ithaca 14853, NY, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca 14853, NY, USA.
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26
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Sommeria-Klein G, Zinger L, Taberlet P, Coissac E, Chave J. Inferring neutral biodiversity parameters using environmental DNA data sets. Sci Rep 2016; 6:35644. [PMID: 27762295 PMCID: PMC5071827 DOI: 10.1038/srep35644] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 10/03/2016] [Indexed: 11/21/2022] Open
Abstract
The DNA present in the environment is a unique and increasingly exploited source of information for conducting fast and standardized biodiversity assessments for any type of organisms. The datasets resulting from these surveys are however rarely compared to the quantitative predictions of biodiversity models. In this study, we simulate neutral taxa-abundance datasets, and artificially noise them by simulating noise terms typical of DNA-based biodiversity surveys. The resulting noised taxa abundances are used to assess whether the two parameters of Hubbell's neutral theory of biodiversity can still be estimated. We find that parameters can be inferred provided that PCR noise on taxa abundances does not exceed a certain threshold. However, inference is seriously biased by the presence of artifactual taxa. The uneven contribution of organisms to environmental DNA owing to size differences and barcode copy number variability does not impede neutral parameter inference, provided that the number of sequence reads used for inference is smaller than the number of effectively sampled individuals. Hence, estimating neutral parameters from DNA-based taxa abundance patterns is possible but requires some caution. In studies that include empirical noise assessments, our comprehensive simulation benchmark provides objective criteria to evaluate the robustness of neutral parameter inference.
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Affiliation(s)
- Guilhem Sommeria-Klein
- Université Toulouse 3 Paul Sabatier, CNRS, UMR 5174 Laboratoire Evolution et Diversité Biologique, F-31062 Toulouse, France
| | - Lucie Zinger
- Université Toulouse 3 Paul Sabatier, CNRS, UMR 5174 Laboratoire Evolution et Diversité Biologique, F-31062 Toulouse, France
| | - Pierre Taberlet
- Université Grenoble Alpes, CNRS, UMR 5553 Laboratoire d’Ecologie Alpine, F-38000 Grenoble, France
| | - Eric Coissac
- Université Grenoble Alpes, CNRS, UMR 5553 Laboratoire d’Ecologie Alpine, F-38000 Grenoble, France
| | - Jérôme Chave
- Université Toulouse 3 Paul Sabatier, CNRS, UMR 5174 Laboratoire Evolution et Diversité Biologique, F-31062 Toulouse, France
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27
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Levi PS, Starnawski P, Poulsen B, Baattrup-Pedersen A, Schramm A, Riis T. Microbial community diversity and composition varies with habitat characteristics and biofilm function in macrophyte-rich streams. OIKOS 2016. [DOI: 10.1111/oik.03400] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Peter S. Levi
- Aquatic Biology; Dept of Bioscience; Aarhus University; Aarhus Denmark
- Environmental Science and Policy, Drake University; Des Moines IA USA
| | - Piotr Starnawski
- Microbiology; Dept of Bioscience; Aarhus University; Aarhus Denmark
| | - Britta Poulsen
- Microbiology; Dept of Bioscience; Aarhus University; Aarhus Denmark
| | | | - Andreas Schramm
- Environmental Science and Policy, Drake University; Des Moines IA USA
| | - Tenna Riis
- Aquatic Biology; Dept of Bioscience; Aarhus University; Aarhus Denmark
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28
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Plante CJ, Fleer V, Jones ML. Neutral processes and species sorting in benthic microalgal community assembly: effects of tidal resuspension. JOURNAL OF PHYCOLOGY 2016; 52:827-839. [PMID: 27373762 DOI: 10.1111/jpy.12445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 05/04/2016] [Indexed: 06/06/2023]
Abstract
Benthic microalgae (BMA) provide vital food resources for heterotrophs and stabilize sediments with their extracellular secretions. A central goal in ecology is to understand how processes such as species interactions and dispersal, contribute to observed patterns of species abundance and distribution. Our objectives were to assess the effects of sediment resuspension on microalgal community structure. We tested whether taxa-abundance distributions could be predicted using neutral community models (NCMs) and also specific hypotheses about passive migration: (i) As migration decreases in sediment patches, BMA α-diversity will decrease, and (ii) As migration decreases, BMA community dissimilarity (β-diversity) will increase. Co-occurrence indices (checkerboard score and variance ratio) were also computed to test for deterministic factors, such as competition and niche differentiation, in shaping communities. Two intertidal sites (mudflat and sand bar) differing in resuspension regime were sampled throughout the tidal cycle. Fluorometry and denaturing gradient gel electrophoresis were utilized to investigate diatom community structure. Observed taxa-abundances fit those predicted from NCMs reasonably well (R2 of 0.68-0.93), although comparisons of observed local communities to artificial randomly assembled communities rejected the null hypothesis that diatom communities were assembled solely by stochastic processes. No co-occurrence tests indicated a significant role for competitive exclusion or niche partitioning in microalgal community assembly. In general, predictions about relationships between migration and species diversity were supported for local community dynamics. BMA at low tide (lowest migration) exhibited reduced α-diversity as compared to periods of immersion at both mudflat and sand bar sites. β-diversity was higher during low tide emersion on the mudflat, but did not differ temporally at the sand bar site. In between-site metacommunity comparisons, low- and high-resuspension sites exhibited distinct community compositions while the low-energy mudflats contained higher microalgal biomass and greater α-diversity. To our knowledge this is the first study to test the relevance of neutral processes in structuring marine microalgal communities. Our results demonstrate a prominent role for stochastic factors in structuring local BMA community assembly, although unidentified nonrandom processes also appear to play some role. High passive migration, in particular, appears to help maintain species diversity and structure communities in both sand and muddy habitats.
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Affiliation(s)
- Craig J Plante
- Grice Marine Laboratory, Biology Dept., College of Charleston, Charleston, South Carolina, 29412, USA
| | - Virginia Fleer
- Coastal Sciences Dept., USM Gulf Coast Research Laboratory, Ocean Springs, Mississippi, 39564, USA
| | - Martin L Jones
- Mathematics Dept., College of Charleston, Charleston, South Carolina, 29424, USA
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29
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Roguet A, Laigle GS, Therial C, Bressy A, Soulignac F, Catherine A, Lacroix G, Jardillier L, Bonhomme C, Lerch TZ, Lucas FS. Neutral community model explains the bacterial community assembly in freshwater lakes. FEMS Microbiol Ecol 2015; 91:fiv125. [PMID: 26472576 DOI: 10.1093/femsec/fiv125] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2015] [Indexed: 11/14/2022] Open
Abstract
Over the past decade, neutral theory has gained attention and recognition for its capacity to explain bacterial community structure (BCS) in addition to deterministic processes. However, no clear consensus has been drawn so far on their relative importance. In a metacommunity analysis, we explored at the regional and local scale the effects of these processes on the bacterial community assembly within the water column of 49 freshwater lakes. The BCS was assessed using terminal restriction fragment length polymorphism (T-RFLP) of the 16S rRNA genes. At the regional scales, results indicated that the neutral community model well predicted the spatial community structure (R(2) mean = 76%) compared with the deterministic factors - which explained only a small fraction of the BCS total variance (less than 14%). This suggests that the bacterial compartment was notably driven by stochastic processes, through loss and gain of taxa. At the local scale, the bacterial community appeared to be spatially structured by stochastic processes (R(2) mean = 65%) and temporally governed by the water temperature, a deterministic factor, even if some bacterial taxa were driven by neutral dynamics. Therefore, at both regional and local scales the neutral community model appeared to be relevant in explaining the bacterial assemblage structure.
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Affiliation(s)
- Adélaïde Roguet
- Laboratoire Eau Environnement et Systèmes Urbains (UMR MA 102), Université Paris-Est, AgroParisTech, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
| | - Grégory S Laigle
- Laboratoire Eau Environnement et Systèmes Urbains (UMR MA 102), Université Paris-Est, AgroParisTech, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
| | - Claire Therial
- Laboratoire Eau Environnement et Systèmes Urbains (UMR MA 102), Université Paris-Est, AgroParisTech, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
| | - Adèle Bressy
- Laboratoire Eau Environnement et Systèmes Urbains (UMR MA 102), Université Paris-Est, AgroParisTech, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
| | - Frédéric Soulignac
- Laboratoire Eau Environnement et Systèmes Urbains (UMR MA 102), Université Paris-Est, AgroParisTech, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
| | - Arnaud Catherine
- Unité Molécules de Communication et Adaptation des Micro-organismes (UMR 7245), Sorbonne Université, Muséum National d'Histoire Naturelle, Case 39, 57 rue Cuvier, FR 75005 Paris, France
| | - Gérard Lacroix
- Institute of Ecology and Environmental Sciences of Paris (UMR 7618 [UPMC, UPEC, Paris Diderot, CNRS, IRD, INRA]), Université Pierre et Marie Curie, Bâtiment A, 7 quai St Bernard, FR 75005 Paris, France CEREEP-Ecotron Ile De France (UMS 3194 [CNRS, ENS]), Ecole Normale Supérieure, 78 rue du Château, 77140 St-Pierre-lès-Nemours, France
| | - Ludwig Jardillier
- Écologie Systématique Évolution, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Céline Bonhomme
- Laboratoire Eau Environnement et Systèmes Urbains (UMR MA 102), Université Paris-Est, AgroParisTech, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
| | - Thomas Z Lerch
- Institute of Ecology and Environmental Sciences of Paris (UMR 7618 [UPMC, UPEC, Paris Diderot, CNRS, IRD, INRA]), Université Paris-Est Créteil, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
| | - Françoise S Lucas
- Laboratoire Eau Environnement et Systèmes Urbains (UMR MA 102), Université Paris-Est, AgroParisTech, Faculté des Sciences et Technologie, 61 avenue du Général de Gaulle, FR 94000 Créteil, France
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30
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Hao YQ, Zhao XF, Zhang DY. Field experimental evidence that stochastic processes predominate in the initial assembly of bacterial communities. Environ Microbiol 2015; 18:1730-9. [PMID: 25809418 DOI: 10.1111/1462-2920.12858] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 03/07/2015] [Indexed: 11/29/2022]
Abstract
To assess the relative importance of environmental selection, dispersal and stochastic processes in structuring ecological communities, we conducted a bacterial community assembly experiment using microcosms filled with sterile liquid medium under field conditions in the Inner Mongolian grasslands. Multiple replicate microcosms containing different carbon substrates were placed at nine locations across three spatial scales (10, 300 and 10 000 m distance between locations) in such a way that the environment of microcosms varies independently of the geographical distance. The operational taxonomic units within the experimental communities were assessed via the terminal restriction fragment length polymorphism techniques on the 10th and 17th days after the onset of the experiment. We found no evidence of distance decay in community similarity, and communities within a given location were more similar to each other regardless of environment than communities at other locations within the same spatial scale. Variance partitioning indicated that location explained more compositional variation in microbial communities than environment, particularly on the 17th day, despite that environment and location in combination could only explain less than half of the total variation. These results suggest that bacterial dispersal is not limited by distance in this experiment, and community assembly in microcosms is not environmentally determined but governed by stochastic processes.
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Affiliation(s)
- Yi-Qi Hao
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Xin-Feng Zhao
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology, Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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31
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Lear G, Bellamy J, Case BS, Lee JE, Buckley HL. Fine-scale spatial patterns in bacterial community composition and function within freshwater ponds. ISME JOURNAL 2014; 8:1715-26. [PMID: 24577354 DOI: 10.1038/ismej.2014.21] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 01/14/2014] [Accepted: 01/19/2014] [Indexed: 12/28/2022]
Abstract
The extent to which non-host-associated bacterial communities exhibit small-scale biogeographic patterns in their distribution remains unclear. Our investigation of biogeography in bacterial community composition and function compared samples collected across a smaller spatial scale than most previous studies conducted in freshwater. Using a grid-based sampling design, we abstracted 100+ samples located between 3.5 and 60 m apart within each of three alpine ponds. For every sample, variability in bacterial community composition was monitored using a DNA-fingerprinting methodology (automated ribosomal intergenic spacer analysis) whereas differences in bacterial community function (that is, carbon substrate utilisation patterns) were recorded from Biolog Ecoplates. The exact spatial position and dominant physicochemical conditions (for example, pH and temperature) were simultaneously recorded for each sample location. We assessed spatial differences in bacterial community composition and function within each pond and found that, on average, community composition or function differed significantly when comparing samples located >20 m apart within any pond. Variance partitioning revealed that purely spatial variation accounted for more of the observed variability in both bacterial community composition and function (range: 24-38% and 17-39%) than the combination of purely environmental variation and spatially structured environmental variation (range: 17-32% and 15-20%). Clear spatial patterns in bacterial community composition, but not function were observed within ponds. We therefore suggest that some of the observed variation in bacterial community composition is functionally 'redundant'. We confirm that distinct bacterial communities are present across unexpectedly small spatial scales suggesting that populations separated by distances of >20 m may be dispersal limited, even within the highly continuous environment of lentic water.
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Affiliation(s)
- Gavin Lear
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Julia Bellamy
- Department of Ecology, Lincoln University, Christchurch, New Zealand
| | - Bradley S Case
- Department of Ecology, Lincoln University, Christchurch, New Zealand
| | - Jack E Lee
- Department of Ecology, Lincoln University, Christchurch, New Zealand
| | - Hannah L Buckley
- Department of Ecology, Lincoln University, Christchurch, New Zealand
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