Prokaryotic and Eukaryotic Communities Characteristic in the Water Column and Sediment along the Xiangjiang River, China

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Abstract

Microbial communities are central components of river ecosystems. They are involved in the transportation and transformation of certain pollutants, including nutrients discharged into surface water. Knowledge of microbial community structures is vital for understanding biochemical circulation in aquatic ecosystems. However, most of the research that is currently being conducted focuses more on bacterial diversity and less on eukaryotes, which also play key roles in the nutrient cycle. In this study, 10 sampling sites along the Xiangjiang River were selected, covering the entire reaches of Changsha City, China. Both prokaryotic and eukaryotic diversity and composition in the water and sediment samples were investigated. The results showed that conductivity, TN, and NH4+-N were the main environmental parameters influencing the distribution of microbial communities in the river water column. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant bacteria in sediments. The most abundant taxa in the water samples were Proteobacteria, Actinobacteria, and Firmicutes, with Chloroplastida being the dominant eukaryote. Eukaryotes in sediments are much spatially stochastic. Function analysis showed that bacteria in the water column had more phototrophic genes than those in the sediment samples, while the latter had more nitrogen-transformation-involved genes. This suggested that river sediment is more active in the global nitrogen cycle, while the overlying water plays an important role in oxygenic photosynthesis.

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Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

J. Gregory Caporaso, Christian L. Lauber, William A. Walters … (2011)

The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.

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Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples.

Alma Parada, David M Needham, Jed Fuhrman (2016)

Microbial community analysis via high-throughput sequencing of amplified 16S rRNA genes is an essential microbiology tool. We found the popular primer pair 515F (515F-C) and 806R greatly underestimated (e.g. SAR11) or overestimated (e.g. Gammaproteobacteria) common marine taxa. We evaluated marine samples and mock communities (containing 11 or 27 marine 16S clones), showing alternative primers 515F-Y (5'-GTGYCAGCMGCCGCGGTAA) and 926R (5'-CCGYCAATTYMTTTRAGTTT) yield more accurate estimates of mock community abundances, produce longer amplicons that can differentiate taxa unresolvable with 515F-C/806R, and amplify eukaryotic 18S rRNA. Mock communities amplified with 515F-Y/926R yielded closer observed community composition versus expected (r(2) = 0.95) compared with 515F-Y/806R (r(2) ∼ 0.5). Unexpectedly, biases with 515F-Y/806R against SAR11 in field samples (∼4-10-fold) were stronger than in mock communities (∼2-fold). Correcting a mismatch to Thaumarchaea in the 515F-C increased their apparent abundance in field samples, but not as much as using 926R rather than 806R. With plankton samples rich in eukaryotic DNA (> 1 μm size fraction), 18S sequences averaged ∼17% of all sequences. A single mismatch can strongly bias amplification, but even perfectly matched primers can exhibit preferential amplification. We show that beyond in silico predictions, testing with mock communities and field samples is important in primer selection.

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A guide to the natural history of freshwater lake bacteria.

Stefan Bertilsson, Ryan J. Newton, Alexander Eiler … (2011)

Freshwater bacteria are at the hub of biogeochemical cycles and control water quality in lakes. Despite this, little is known about the identity and ecology of functionally significant lake bacteria. Molecular studies have identified many abundant lake bacteria, but there is a large variation in the taxonomic or phylogenetic breadths among the methods used for this exploration. Because of this, an inconsistent and overlapping naming structure has developed for freshwater bacteria, creating a significant obstacle to identifying coherent ecological traits among these groups. A discourse that unites the field is sorely needed. Here we present a new freshwater lake phylogeny constructed from all published 16S rRNA gene sequences from lake epilimnia and propose a unifying vocabulary to discuss freshwater taxa. With this new vocabulary in place, we review the current information on the ecology, ecophysiology, and distribution of lake bacteria and highlight newly identified phylotypes. In the second part of our review, we conduct meta-analyses on the compiled data, identifying distribution patterns for bacterial phylotypes among biomes and across environmental gradients in lakes. We conclude by emphasizing the role that this review can play in providing a coherent framework for future studies.