Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau

Xiong, Jinbo; Liu, Yongqin; Lin, Xiangui; Zhang, Huayong; Zeng, Jun; Hou, Juzhi; Yang, Yongping; Yao, Tandong; Knight, Rob; Chu, Haiyan

doi:10.1111/j.1462-2920.2012.02799.x

Cited by 512 publications

(306 citation statements)

References 46 publications

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“…However, for larger spatial extents similar to those we considered here, former reports indicate that the bacterial distance-decay relationships range from significant in lake surface sediments across the Tibetan Plateau (Xiong et al, 2012) to nonsignificant in North America soils (Fierer and Jackson, 2006). These results collectively suggest that the rate of distancedecay in bacteria shows strong context-dependency, potentially driven by among-habitat variation in the degree of environmental spatial autocorrelation and in the degree of dispersal limitation.…”

Section: Phylogenetic Signal Varies With Phylogenetic Distancesupporting

confidence: 76%

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

et al. 2013

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Increasing evidence has emerged for non-random spatial distributions of microbes, but knowledge of the processes that cause variation in microbial assemblage among ecosystems is lacking. For instance, some studies showed that deterministic processes such as habitat specialization are important, while other studies hold that bacterial communities are assembled by stochastic forces. Here we examine the relative influence of deterministic and stochastic processes for bacterial communities from subsurface environments, stream biofilm, lake water, lake sediment and soil using pyrosequencing of the 16S ribosomal RNA gene. We show that there is a general pattern in phylogenetic signal in species ecological niches across recent evolutionary time for all studied habitats, enabling us to infer the influences of community assembly processes from patterns of phylogenetic turnover in community composition. The phylogenetic dissimilarities among-habitat types were significantly higher than within them, and the communities were clustered according to their original habitat types. For communities within-habitat types, the highest phylogenetic turnover rate through space was observed in subsurface environments, followed by stream biofilm on mountainsides, whereas the sediment assemblages across regional scales showed the lowest turnover rate. Quantifying phylogenetic turnover as the deviation from a null expectation suggested that measured environmental variables imposed strong selection on bacterial communities for nearly all sample groups. For three sample groups, spatial distance reflected unmeasured environmental variables that impose selection, as opposed to spatial isolation. Such characterization of spatial and environmental variables proved essential for proper interpretation of partial Mantel results based on observed beta diversity metrics. In summary, our results clearly indicate a dominant role of deterministic processes on bacterial assemblages and highlight that bacteria show strong habitat associations that have likely emerged through evolutionary adaptation.

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Section: Phylogenetic Signal Varies With Phylogenetic Distancesupporting

confidence: 76%

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

et al. 2013

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“…Recent studies have shown that shifts in the structure of bacterial communities can be associated with changes in a number of soil physicochemistry including soil texture (Sessitsch et al 2001;Kim et al 2013), soil pH (Mannisto et al 2007;Lauber et al 2008;Xiong et al 2012), soil moisture , temperature (Lipson 2007), and soil nitrogen (Frey et al 2004;Nilsson et al 2007). From the baseband to the top of the mountain, environmental factors (including soil physicochemistry, plant and climate) change sharply (Korner 2007), indicating that bacterial distributions may exhibit differently owe to variations of environmental factors.…”

Section: Introductionmentioning

confidence: 99%

A hollow bacterial diversity pattern with elevation in Wolong Nature Reserve, Western Sichuan Plateau

Liu

Shi

et al. 2016

J Soils Sediments

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Purpose The pattern of eukaryotic macroorganisms varies with altitude is well-documented; by contrast, very little is known of how a bacterial pattern in soils varies with the elevation in a montane ecosystem. Mostly, previous studies on soil bacteria have either found a diversity decline, no trend, or a hump-back trend with increasing elevation. The aim of this study was to investigate the bacterial community composition and diversity patterns of Mount Nadu in Wolong Nature Reserve, Western Sichuan Plateau (3000-3945 masl). Materials and methods In total, 30 soil samples from the mountain at 10 sampling elevational zones (every 100 m from the baseband to the summit) were collected. High-throughput pyrosequencing approach was performed of soil bacterial 16S rRNA targeting V3 + V4 region by MiSeq PE300 and taxonomically classified based on Silva database. Bacterial community composition and diversity patterns were detected, and bacterial data were correlated with environmental factors to determine which factors influenced bacterial community composition. Results and discussion We obtained an average of 30,172 sequences per soil and found that the relative abundance of Acidobacteria and Proteobacteria count more than 70 % of the whole bacteria. Cooperative network analysis also revealed that Acidobacteria and Proteobacteria were important hubs in the community. Bacterial diversity pattern was found to be a significant hollow trend along altitudinal gradients and diversity of the dominant phyla (e.g., Acidobacteria, Proteobacteria) followed the results of the whole bacterial diversity. Moreover, distancebased linear model identified that soil pH and TN significantly provided 7.40 and 6.01 % of the total variation. Conclusions The hollow trend of bacterial diversity has rarely been observed in nature. It indicated that no unifying bacterial diversity pattern can be expected along elevational gradients among the mountain system, and our result suggested the importance of environmental factors in structuring bacterial communities in this montane ecosystem.

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“…(5 -CCGTCAATTCMTTTRAGTTT-3 ) [22] were used to amplify the V4-V5 region of the bacterial 16S rRNA gene. DNA amplicons were separated by electrophoresis on a 2% (w/v) agarose gel and recovered using an AxyPrep DNA Gel Extraction Kit (Axygen Ltd., Hangzhou City, China).…”

Section: High-throughput Sequencingmentioning

confidence: 99%

Characterization of a Microbial Community in an Anammox Process Using Stored Anammox Sludge

Chen

Dai

Cao

et al. 2017

Water

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This study investigated a rapid start-up anaerobic ammonium oxidation (Anammox) process by inoculation with stored Anammox sludge and characterized the associated microbial communities. The Anammox process took only 43 days to start. A high nitrogen removal rate of 1.13 kg N m −3 d −1 and a nitrogen loading rate of 1.28 kg N m −3 d −1 were achieved. The ratio of ammonium removal to nitrite removal to nitrate production (1:1:0.2) was slightly lower than the theoretical value, which indicated nitrogen removal by denitrification in the reactor. Illumina high-throughput sequencing of sludge samples confirmed the co-existence of Anammox bacteria and denitrifying bacteria in the reactor and demonstrated that denitrifying bacteria play a role in nitrogen removal during the Anammox process. The dominant microbes in the reactor were Proteobacteria, Chlorobi, Chloroflexi, and Planctomycetes. However, only one species of Anammox bacteria, Candidatus jettenia, was identified and had an abundance of 4.92%. Our results illustrate the relationship between Anammox reactor performance and microbial community succession.

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Geographic distance and pH drive bacterial distribution in alkaline lake sediments across Tibetan Plateau

Cited by 512 publications

References 46 publications

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

Phylogenetic beta diversity in bacterial assemblages across ecosystems: deterministic versus stochastic processes

A hollow bacterial diversity pattern with elevation in Wolong Nature Reserve, Western Sichuan Plateau

Characterization of a Microbial Community in an Anammox Process Using Stored Anammox Sludge

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