Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems

Zinger, Lucie; Amaral‐Zettler, Linda; Fuhrman, Jed A.; Horner-Devine, M. Claire; Huse, Susan M.; Welch, David; Martiny, Jennifer B. H.; Sogin, Mitchell L.; Boetius, Antje; Ramette, Alban

doi:10.1371/journal.pone.0024570

Cited by 522 publications

(509 citation statements)

References 68 publications

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“…As a mixing environment between terrestrial and marine habitats, the coastal area is thought to have a significantly higher diversity of bacterial community than marine sediment (Allen et al 2009;Zinger et al 2011). Our results identified 17 bacterial phyla in the sediments of Jiaozhou Bay.…”

Section: Bacterial Taxonomic Diversity In Jiaozhou Bay Sedimentsmentioning

confidence: 65%

Bacterial composition and spatiotemporal variation in sediments of Jiaozhou Bay, China

Liu

et al. 2014

J Soils Sediments

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Purpose Although coastal marine sediments harbor diverse bacteria with important ecological and environmental functions, a comprehensive view of their community characteristics is still lacking in typical environments along the China coast. We studied the diversity and composition of bacterial community in the sediment of Jiaozhou Bay and characterized their spatiotemporal patterns, aiming to analyze the effects of geographic heterogeneity, seasonal difference, anthropogenic activity, and eutrophication gradient on the bacterial ecology. Materials and methods Sixteen full-length bacterial 16S rRNA gene clone libraries were constructed from the sediment bacteria at four stations (A5, B2, D1, and D7) of Jiaozhou Bay over four seasons (February, May, August, and November). The bacterial diversity and community structure variation were analyzed. Results and discussion A total of 1088 16S rRNA gene sequences and 746 distinct operational taxonomic units (OTUs) (at 97 % sequence similarity level) were retrieved from the 16 clone libraries. Libraries of each sample revealed a high diversity, and a total of 17 bacterial phyla were identified.Bacteria lineages Proteobacteria (mostly γ-Proteobacteria and δ-Proteobacteria), Actinobacteria, Bacteroidetes, and Planctomycetes, which are commonly found in marine sediments, were the dominant divisions in our samples. Meanwhile, some uncommon phyla, such as Deinococcus-Thermus and Lentisphaerae, were also detected. Distinct spatial patterns and noticeable seasonal variations of bacteria community were observed, indicating that environmental heterogeneity in spatial variation other than in temporal variation may be more important in determining the bacterial communities. Most of the abundant OTUs were related to sequences retrieved from the heavy-metal-polluted environments, indicating that the Jiaozhou Bay might be influenced by pollution. Conclusions The bacterial communities in Jiaozhou Bay sediments are highly diverse. The four typical stations that we chose might experience different anthropogenic effects and eutrophication gradients, which shaped their bacterial community composition. The environment of Jiaozhou Bay may be under pressure exerted by multi-dimension anthropogenic activities. This study provided a novel insight into the bacterial community variations in Jiaozhou Bay, enriching knowledge about ecological bioindicators and mechanisms that maintain bacterial diversity and shape bacterial community composition.

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Section: Bacterial Taxonomic Diversity In Jiaozhou Bay Sedimentsmentioning

confidence: 65%

Bacterial composition and spatiotemporal variation in sediments of Jiaozhou Bay, China

Liu

et al. 2014

J Soils Sediments

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“…Sequences, which could not be assigned to bacteria or archaea, were discarded. OTUs were defined using a distance matrix with 3% dissimilarity (Zinger et al 2011). Data analysis was performed using mothur software package version 1.31.2 (http://www.mothur.org/) following the standard operational procedure (SOP) (Schloss et al 2009).…”

Section: Illumina Amplicon Sequencingmentioning

confidence: 99%

The effect of crop rotation between wetland rice and upland maize on the microbial communities associated with roots

et al. 2017

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Background and aims Microorganisms colonize plant roots for mutual benefits. Colonization is initiated by the soil microbial community but is also affected by soil conditions and plant type. Rice typically grows under wetland conditions that are anoxic, thus being supportive for an anaerobic methanogenic microbial community. Maize, however, grows under upland conditions that are oxic, thus being supportive for an aerobic microbial community. Crop rotation between wetland rice and upland maize is not uncommon, but the effect of this management on microbial colonization of plant roots is largely unknown and was the aim of our study. Methods We used the roots of rice and maize from a two-year study in the Philippines, where on the same soil wetland rice was cultivated either in both wet and dry season or was rotated with upland maize in the dry season. The microbial colonization of the root ecto-and endorhizosphere was assessed by using quantitative PCR and illumina sequencing of the bacterial and archaeal 16S rRNA genes. Results The data showed that maize roots had completely different microbial community structures than the rice roots from continuous wetland cultivation, while rice roots from crop rotation were in-between. These effects of management were seen for each of the different bacterial phyla. For example, among the most abundant operational taxonomic units (OTUs) Firmicutes, Deltaproteobacteria and the methanogenic Methanocella spp. were less abundant while Alphaproteobacteria and the methanogenic Methanobacterium spp. were more abundant on maize than on rice roots. Conclusions Our study showed that root colonization by Archaea and Bacteria was strongly affected by crop rotation between wetland rice and upland maize.

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“…The present study shows that Acidobacteria and Proteobacteria are also predominant in the soil of tropical forests in Indonesia (Java and Sumatra) and Singapore in Southeast Asia. Acidobacteria and Proteobacteria are Gram-negative bacteria represented by many species that grow and survive under many environmental conditions (Stackebrandt et al, 1988;Quaiser et al, 2003); however, Acidobacteria are found primarily in soil (Sogins et al, 2006), while Proteobacteria are found in soil (Barns et al, 1999;Zinger et al, 2011;Wang et al, 2012), fresh water (Hugenholtz et al, 1998) and seawater (Hugenholtz et al, 1998;Venter et al, 2004;Zinger et al, 2011). In BKOman, an exceptional phylum composition was observed, characterized by high representation of Proteobacteria (≈40%) and low representation of Acidobacteria (4%).…”

Section: Discussionmentioning

confidence: 99%

Geographical variation in soil bacterial community structure in tropical forests in Southeast Asia and temperate forests in Japan based on pyrosequencing analysis of 16S rRNA

et al. 2017

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Geographical variation in soil bacterial community structure in 26 tropical forests in Southeast Asia (Malaysia, Indonesia and Singapore) and two temperate forests in Japan was investigated to elucidate the environmental factors and mechanisms that influence biogeography of soil bacterial diversity and composition. Despite substantial environmental differences, bacterial phyla were represented in similar proportions, with Acidobacteria and Proteobacteria the dominant phyla in all forests except one mangrove forest in Sarawak, although highly significant heterogeneity in frequency of individual phyla was detected among forests. In contrast, species diversity (α-diversity) differed to a much greater extent, being nearly six-fold higher in the mangrove forest (Chao1 index = 6,862) than in forests in Singapore and Sarawak (~1,250). In addition, natural mixed dipterocarp forests had lower species diversity than acacia and oil palm plantations, indicating that aboveground tree composition does not influence soil bacterial diversity. Shannon and Chao1 indices were correlated positively, implying that skewed operational taxonomic unit (OTU) distribution was associated with the abundance of overall and rare (singleton) OTUs. No OTUs were represented in all 28 forests, and forest-specific OTUs accounted for over 70% of all detected OTUs. Forests that were geographically adjacent and/or of the same forest type had similar bacterial species composition, and a positive correlation was detected between species divergence (β-diversity) and direct distance between forests. Both α-and β-diversities were correlated with soil pH. These results suggest that soil bacterial communities in different forests evolve largely independently of each other and that soil bacterial communities adapt to their local environment, modulated by bacterial dispersal (distance effect) and forest type. Therefore, we conclude that the biogeography of soil bacteria communities described here is non-random, reflecting the influences of contemporary environmental factors and evolutionary history.

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Global Patterns of Bacterial Beta-Diversity in Seafloor and Seawater Ecosystems

Cited by 522 publications

References 68 publications

Bacterial composition and spatiotemporal variation in sediments of Jiaozhou Bay, China

Bacterial composition and spatiotemporal variation in sediments of Jiaozhou Bay, China

The effect of crop rotation between wetland rice and upland maize on the microbial communities associated with roots

Geographical variation in soil bacterial community structure in tropical forests in Southeast Asia and temperate forests in Japan based on pyrosequencing analysis of 16S rRNA

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