Dataset Information

Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients.

ABSTRACT: The significance of salinity in shaping bacterial communities dwelling in estuarine areas has been well documented. However, the influences of other environmental factors such as dissolved oxygen and nutrients in determining distribution patterns of both individual taxa and bacterial communities inhabited local estuarine regions remain elusive. Here, bacterioplankton community structures of surface and bottom waters from eight sites along the Pearl Estuary were characterized with 16S rRNA gene pyrosequencing. The results showed significant differences of bacterioplankton community between freshwater and saltwater sites, and further between surface and bottom waters of saltwater sites. Synechococcus dominated the surface water of saltwater sites while Oceanospirillales, SAR11 and SAR406 were prevalent in the bottom water. Betaproteobacteria was abundant in freshwater sites, with no significant difference between water layers. Occurrence of phylogenetic shifts in taxa affiliated to the same clade was also detected. Dissolved oxygen explained most of the bacterial community variation in the redundancy analysis targeting only freshwater sites, whereas nutrients and salinity explained most of the variation across all samples in the Pearl Estuary. Methylophilales (mainly PE2 clade) was positively correlated to dissolved oxygen, whereas Rhodocyclales (mainly R.12up clade) was negatively correlated. Moreover, high nutrient inputs to the freshwater area of the Pearl Estuary have shifted the bacterial communities toward copiotrophic groups, such as Sphingomonadales. The present study demonstrated that the overall nutrients and freshwater hypoxia play important roles in determining bacterioplankton compositions and provided insights into the potential ecological roles of specific taxa in estuarine environments.

SUBMITTER: Liu J

PROVIDER: S-EPMC4322608 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients.

Liu Jiwen J Fu Bingbing B Yang Hongmei H Zhao Meixun M He Biyan B Zhang Xiao-Hua XH

Frontiers in microbiology 20150210

The significance of salinity in shaping bacterial communities dwelling in estuarine areas has been well documented. However, the influences of other environmental factors such as dissolved oxygen and nutrients in determining distribution patterns of both individual taxa and bacterial communities inhabited local estuarine regions remain elusive. Here, bacterioplankton community structures of surface and bottom waters from eight sites along the Pearl Estuary were characterized with 16S rRNA gene p ...[more]

PMID: 25713564

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Project description:Phytoplankton and bacterioplankton play significant roles in estuarine systems. It is important to demonstrate the spatial variability of bacterial and microalgal communities and understand the co-acclimation of these organisms to different environmental factors. In this study, MiSeq sequencing and morphological identification were applied to analyze the variations in bacterial and microalgal communities in the Pearl River Estuary, respectively. Molecular ecological network analysis was used to investigate the potential interactions between microalgae and bacteria and illustrate the responses of these interactions to environmental gradients. The results revealed that microalgal/bacterial communities in freshwater samples were distinct from those in mesohaline water samples. Microalgae affiliated to the genus Skeletonema dominated the mesohaline water phytoplankton communities, while Melosira was the more abundant genus in freshwater communities. Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Acidimicrobiia dominated bacterial communities in freshwater samples, while Gammaproteobacteria, Bacilli, and Synechococcophycideae were more abundant in mesohaline water samples. Tightly correlations were observed between phytoplankton and bacterioplankton. These interactions were regarded to be key factors in shaping the community structures. Further, the KEGG database and PICRUSt were used to predict the functions of bacterioplankton in the process of nitrogen cycling. The results indicated that denitrification could play an important role in nitrogen loss and might alleviate the eutrophication in the Pearl River Estuary. Collectively, the results in this study revealed that substantial changes in phytoplankton and bacterioplankton communities were correlated with the gradients of environmental parameters in the Pearl River Estuary. The results also demonstrated that the interactions between phytoplankton and bacterioplankton were important for these organisms to acclimate to changing environments.

Project description:Chesapeake Bay, the largest estuary in North America, can be characterized as having steep and opposing gradients in salinity and dissolved inorganic nitrogen along the main axis of the Bay. In this study, the diversity of nirS gene fragments (encoding cytochrome cd 1-type nitrite reductase), physical/chemical parameters, and benthic N2-fluxes were analyzed in order to determine how denitrifier communities and biogeochemical activity vary along the estuary salinity gradient. The nirS gene fragments were PCR-amplified, cloned, and sequenced from sediment cores collected at five stations. Sequence analysis of 96-123 nirS clones from each station revealed extensive overall diversity in this estuary, as well as distinct spatial structure in the nirS sequence distributions. Both nirS-based richness and community composition varied among stations, with the most dramatic shifts occurring between low-salinity (oligohaline) and moderate-salinity (mesohaline) sites. For four samples collected in April, the nirS-based richness, nitrate concentrations, and N2-fluxes all decreased in parallel along the salinity gradient from the oligohaline northernmost station to the highest salinity (polyhaline) station near the mouth of the Bay. The vast majority of the 550 nirS sequences were distinct from cultivated denitrifiers, although many were closely related to environmental clones from other coastal and estuarine systems. Interestingly, 8 of the 172 OTUs identified accounted for 42% of the total nirS clones, implying the presence of a few dominant and many rare genotypes, which were distributed in a non-random manner along the salinity gradient of Chesapeake Bay. These data, comprising the largest dataset to investigate nirS clone sequence diversity from an estuarine environment, also provided information that was required for the development of nirS microarrays to investigate the interaction of microbial diversity, environmental gradients, and biogeochemical activity.

Project description:We analyzed the phylogenetic composition of bacterioplankton assemblages in 11 Arctic Ocean samples collected over three seasons (winter-spring 1995, summer 1996, and summer-fall 1997) by sequencing cloned fragments of 16S rRNA genes. The sequencing effort was directed by denaturing gradient gel electrophoresis (DGGE) screening of samples and the clone libraries. Sequences of 88 clones fell into seven major lineages of the domain Bacteria: alpha(36%)-, gamma(32%)-, delta(14%)-, and epsilon(1%)-Proteobacteria; Cytophaga-Flexibacter-Bacteroides spp. (9%); Verrucomicrobium spp. (6%); and green nonsulfur bacteria (2%). A total of 34% of the cloned sequences (excluding clones in the SAR11 and Roseobacter groups) had sequence similarities that were <94% compared to previously reported sequences, indicating the presence of novel sequences. DGGE fingerprints of the selected samples showed that most of the bands were common to all samples in all three seasons. However, additional bands representing sequences related to Cytophaga and Polaribacter species were found in samples collected during the summer and fall. Of the clones in a library generated from one sample collected in spring of 1995, 50% were the same and were most closely affiliated (99% similarity) with Alteromonas macleodii, while 50% of the clones in another sample were most closely affiliated (90 to 96% similarity) with Oceanospirillum sp. The majority of the cloned sequences were most closely related to uncultured, environmental sequences. Prominent among these were members of the SAR11 group. Differences between mixed-layer and halocline samples were apparent in DGGE fingerprints and clone libraries. Sequences related to alpha-Proteobacteria (dominated by SAR11) were abundant (52%) in samples from the mixed layer, while sequences related to gamma-proteobacteria were more abundant (44%) in halocline samples. Two bands corresponding to sequences related to SAR307 (common in deep water) and the high-G+C gram-positive bacteria were characteristic of the halocline samples.

Dataset Information

Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients.

Publications

Phylogenetic shifts of bacterioplankton community composition along the Pearl Estuary: the potential impact of hypoxia and nutrients.

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