Biogeography of bacterial communities exposed to progressive long-term environmental change
TL;DR: In this article, the authors studied bacterioplankton communities in a unique system of coastal Antarctic lakes that were exposed to progressive long-term environmental change, using 454 pyrosequencing of the 16S rDNA gene (V3-V4 regions).
Abstract: The response of microbial communities to long-term environmental change is poorly understood. Here, we study bacterioplankton communities in a unique system of coastal Antarctic lakes that were exposed to progressive long-term environmental change, using 454 pyrosequencing of the 16S rDNA gene (V3–V4 regions). At the time of formation, most of the studied lakes harbored marine-coastal microbial communities, as they were connected to the sea. During the past 20 000 years, most lakes isolated from the sea, and subsequently they experienced a gradual, but strong, salinity change that eventually developed into a gradient ranging from freshwater (salinity 0) to hypersaline (salinity 100). Our results indicated that present bacterioplankton community composition was strongly correlated with salinity and weakly correlated with geographical distance between lakes. A few abundant taxa were shared between some lakes and coastal marine communities. Nevertheless, lakes contained a large number of taxa that were not detected in the adjacent sea. Abundant and rare taxa within saline communities presented similar biogeography, suggesting that these groups have comparable environmental sensitivity. Habitat specialists and generalists were detected among abundant and rare taxa, with specialists being relatively more abundant at the extremes of the salinity gradient. Altogether, progressive long-term salinity change appears to have promoted the diversification of bacterioplankton communities by modifying the composition of ancestral communities and by allowing the establishment of new taxa.
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Spanish National Research Council1, Centre national de la recherche scientifique2, Pierre-and-Marie-Curie University3, American Museum of Natural History4, Kaiserslautern University of Technology5, University of Nice Sophia Antipolis6, Aix-Marseille University7, University of Oslo8, Stazione Zoologica Anton Dohrn9, Tokyo Institute of Technology10, University of Geneva11, IFREMER12, University of Exeter13
TL;DR: The authors investigated abundant and rare subcommunities of marine microbial eukaryotes, a crucial group of organisms that remains among the least-explored biodiversity components of the biosphere.
375 citations
TL;DR: The results showed that the geographical patterns of abundant and rare bacterial subcommunities were generally similar, and both of them showed a significant distance–decay relationship, suggesting that the rare bacterial biosphere is not a random assembly, as some authors have assumed, and that its distribution is most likely subject to the same ecological processes that control abundant taxa.
Abstract: Bacteria play key roles in the ecology of both aquatic and terrestrial ecosystems; however, little is known about their diversity and biogeography, especially in the rare microbial biosphere of inland freshwater ecosystems. Here we investigated aspects of the community ecology and geographical distribution of abundant and rare bacterioplankton using high-throughput sequencing and examined the relative influence of local environmental variables and regional (spatial) factors on their geographical distribution patterns in 42 lakes and reservoirs across China. Our results showed that the geographical patterns of abundant and rare bacterial subcommunities were generally similar, and both of them showed a significant distance–decay relationship. This suggests that the rare bacterial biosphere is not a random assembly, as some authors have assumed, and that its distribution is most likely subject to the same ecological processes that control abundant taxa. However, we identified some differences between the abundant and rare groups as both groups of bacteria showed a significant positive relationship between sites occupancy and abundance, but the abundant bacteria exhibited a weaker distance–decay relationship than the rare bacteria. Our results implied that rare subcommunities were mostly governed by local environmental variables, whereas the abundant subcommunities were mainly affected by regional factors. In addition, both local and regional variables that were significantly related to the spatial variation of abundant bacterial community composition were different to those of rare ones, suggesting that abundant and rare bacteria may have discrepant ecological niches and may play different roles in natural ecosystems.
365 citations
Cites background from "Biogeography of bacterial communiti..."
...Recent high-throughput sequencing studies indicated that the ‘rare biosphere’ fraction of the bacterial community follows biogeographical patterns similar to those of the most abundant members of the community and have distinct spatial distribution patterns in Arctic Ocean and coastal Antarctic lakes (Galand et al., 2009; Logares et al., 2013)....
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...…that the ‘rare biosphere’ fraction of the bacterial community follows biogeographical patterns similar to those of the most abundant members of the community and have distinct spatial distribution patterns in Arctic Ocean and coastal Antarctic lakes (Galand et al., 2009; Logares et al., 2013)....
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...Recent studies using high-throughput sequencing in Arctic Ocean and coastal Antarctic lakes demonstrated that rare bacteria had distinct spatial distribution patterns, and showed a similar spatial pattern to the abundant bacterial subcommunity (Galand et al., 2009; Logares et al., 2013)....
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TL;DR: A review of the available research on how salt affects decomposer microbial communities and carbon cycling in soil can be found in this paper, where the authors provide a brief overview and qualification of widely applied methods to assess microorganisms in soil to date.
Abstract: Salinization of soil is recognised as one of the most pressing environmental challenges to resolve for the next century. We here conduct a synoptic review of the available research on how salt affects decomposer microbial communities and carbon (C) cycling in soil. After summarizing known physiological responses of microorganisms to salinity, we provide a brief overview and qualification of a selection of widely applied methods to assess microorganisms in soil to date. The dominant approaches to characterise microbial responses to salt exposure have so far been microbial biomass and respiration measurements. We compile datasets from a selection of studies and find that (1) microbial biomass-carbon (C) per C held in soil organic matter shows no consistent pattern with long-term (field gradients) or short-term (laboratory additions) soil salinity level, and (2) respiration per soil organic C is substantially inhibited by higher salt concentrations in soil, and consistently so for both short-term and long-term salinity levels. Patterns that emerge from extra-cellular enzyme assessments are more difficult to generalize, and appear to vary with the enzyme studied, and its context. Growth based assessments of microbial responses to salinization are largely lacking. Relating the established responses of microbial respiration to that of growth could provide an estimate for how the microbial C-use efficiency would be affected by salt exposure. This would be a valuable predictor for changes in soil C sequestration. A few studies have investigated the connection between microbial tolerance to salt and the soil salinity levels, but so far results have not been conclusive. We predict that more systematic inquiries including comprehensive ranges of soil salinities will substantiate a connection between soil salinity and microbial tolerance to salt. This would confirm that salinity has a direct effect on the composition of microbial communities. While salt has been identified as one of the most powerful environmental factors to structure microbial communities in aquatic environments, no up-to-date sequence based assessments currently exist from soil. Filling this gap should be a research priority. Moreover, linking sequencing based assessments of microbial communities to their tolerance to salt would have the potential to yield biomarker sets of microbial sequences. This could provide predictive power for, e.g., the sensitivity of agricultural soils to salt exposure, and, as such, a useful tool for soil resource management. We conclude that salt exposure has a powerful influence on soil microbial communities and processes. In addition to being one of the most pressing agricultural problems to solve, this influence could also be used as an experimental probe to better understand how microorganisms control the biogeochemistry in soil. (C) 2014 Elsevier Ltd. All rights reserved. (Less)
336 citations
01 Jan 2014
TL;DR: It is proposed that marine planktonic microeukaryote assemblages incorporate dynamic and metabolically active abundant and rare subcommunities, with contrasting structuring patterns but fairly regular proportions, across space and time.
Abstract: Biosciences, University of Exeter, Geoffrey Pope Building,Exeter EX4 4QD, UKSummaryBackground: Biological communities are normally composedof a few abundant and many rare species. This pattern isparticularly prominent in microbial communities, in whichmost constituent taxa are usually extremely rare. Althoughabundant and rare subcommunities may present intrinsiccharacteristics that could be crucial for understandingcommunity dynamics and ecosystem functioning, microbiolo-gists normally do not differentiate between them. Here, weinvestigate abundant and rare subcommunities of marinemicrobial eukaryotes, a crucial group of organisms thatremains among the least-explored biodiversity componentsof the biosphere. We surveyed surface waters of sixseparate coastal locations in Europe, independently consid-ering the picoplankton, nanoplankton, and microplankton/mesoplankton organismal size fractions.Results: Deep Illumina sequencing of the 18S rRNA indicatedthat the abundant regional community was mostly structuredby organismal size fraction, whereas the rare regional com-munity was mainly structured by geographic origin. However,someabundantandraretaxapresentedsimilarbiogeography,pointing to spatiotemporal structure in the rare microeukar-yote biosphere. Abundant and rare subcommunities pre-sented regular proportions across samples, indicating similarspecies-abundancedistributionsdespitetaxonomiccomposi-tional variation. Several taxa were abundant in one locationand rare in other locations, suggesting large oscillations inabundance. The substantial amount of metabolically activelineages found in the rare biosphere suggests that this sub-community constitutes a diversity reservoir that can respondrapidly to environmental change.Conclusions:Weproposethatmarineplanktonicmicroeukar-yote assemblages incorporate dynamic and metabolicallyactive abundant and rare subcommunities, with contrastingstructuring patterns but fairly regular proportions, acrossspace and time.IntroductionMicrobes are the dominant form of life in the oceans, playingfundamental roles in ecosystem functioning and biogeo-chemicalprocessesonlocalandglobalscales[1–4].However,limited knowledge of their diversity and community structureacross space and time [5, 6] hinders our understanding ofthe links between microbial life and ecosystem functioning[7]. During the last decade, technological progress in molecu-lar ecology and environmental sequencing has substantiallyboosted our understanding of marine microbes, unveilingnotable patterns of abundant and rare subcommunities[4, 8, 9], reminiscent of patterns observed in classical plantandanimalecology[10].Therecentlydiscoveredlargeamountof rare taxa in microbial communities is now referred to as the‘‘rare biosphere’’ [11], and its exploration is made feasibletodaybymeansofhigh-throughputsequencing(HTS)technol-ogies [12].Abundant and rare microbial subcommunities may havefundamentally different characteristics and ecological roles.For example, rare marine microbes are hypothesized toinclude ecologically redundant taxa that could increase inabundance following environmental perturbation or changeand maintain continuous ecosystem functioning [13]. Locallyrare taxa can also act as seeds for seasonal succession orsporadic blooms. Conversely, the drastic decrease in abun-dance or even extinction of a globally abundant oceanicmicrobe with no ecologically comparable counterpart in therare biosphere could have significant and unpredictable
332 citations
Cites background or result from "Biogeography of bacterial communiti..."
...Comparable results have been reported for marine and lacustrine prokaryotes [17, 19, 38]....
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...Both abundant and rare bacteria can present similar biogeographic patterns [17, 19], indicating similar community assembly mechanisms....
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References
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Journal Article•
TL;DR: Copyright (©) 1999–2012 R Foundation for Statistical Computing; permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and permission notice are preserved on all copies.
Abstract: Copyright (©) 1999–2012 R Foundation for Statistical Computing. Permission is granted to make and distribute verbatim copies of this manual provided the copyright notice and this permission notice are preserved on all copies. Permission is granted to copy and distribute modified versions of this manual under the conditions for verbatim copying, provided that the entire resulting derived work is distributed under the terms of a permission notice identical to this one. Permission is granted to copy and distribute translations of this manual into another language, under the above conditions for modified versions, except that this permission notice may be stated in a translation approved by the R Core Team.
272,030 citations
"Biogeography of bacterial communiti..." refers background or methods in this paper
...The ISME Journal (2013) 7, 937–948; doi:10.1038/ismej.2012.168; published online 20 December 2012 Subject Category: microbial population and community ecology Keywords: Antarctica; Bacteria; environmental change; long-term; pyrosequencing; salinity...
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...All computations were done in R (R-DevelopmentCore-Team, 2008)....
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TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Abstract: Supplementary Figure 1 Overview of the analysis pipeline. Supplementary Table 1 Details of conventionally raised and conventionalized mouse samples. Supplementary Discussion Expanded discussion of QIIME analyses presented in the main text; Sequencing of 16S rRNA gene amplicons; QIIME analysis notes; Expanded Figure 1 legend; Links to raw data and processed output from the runs with and without denoising.
28,911 citations
"Biogeography of bacterial communiti..." refers background or methods in this paper
...During the past 20 000 years, most lakes isolated from the sea, and subsequently they experienced a gradual, but strong, salinity change that eventually developed into a gradient ranging from freshwater (salinity 0) to hypersaline (salinity 100)....
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Journal Article•
TL;DR: PAST (PAleontological STatistics) as discussed by the authors is a simple-to-use software package for executing a range of standard numerical analysis and operations used in quantitative paleontology.
Abstract: A comprehensive, but simple-to-use software package for executing a range of standard numerical analysis and operations used in quantitative paleontology has been developed. The program, called PAST (PAleontological STatistics), runs on standard Windows computers and is available free of charge. PAST integrates spreadsheet-type data entry with univariate and multivariate statistics, curve fitting, timeseries analysis, data plotting, and simple phylogenetic analysis. Many of the functions are specific to paleontology and ecology, and these functions are not found in standard, more extensive, statistical packages. PAST also includes fourteen case studies (data files and exercises) illustrating use of the program for paleontological problems, making it a complete educational package for courses in quantitative methods.
19,926 citations
"Biogeography of bacterial communiti..." refers methods in this paper
..., 2008) or in PAST (Hammer et al., 2001)....
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TL;DR: UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters and offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Abstract: Motivation: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification.
Results: UBLAST and USEARCH are new algorithms enabling sensitive local and global search of large sequence databases at exceptionally high speeds. They are often orders of magnitude faster than BLAST in practical applications, though sensitivity to distant protein relationships is lower. UCLUST is a new clustering method that exploits USEARCH to assign sequences to clusters. UCLUST offers several advantages over the widely used program CD-HIT, including higher speed, lower memory use, improved sensitivity, clustering at lower identities and classification of much larger datasets.
Availability: Binaries are available at no charge for non-commercial use at http://www.drive5.com/usearch
Contact: [email protected]
Supplementary information:Supplementary data are available at Bioinformatics online.
17,301 citations