Bacterial diversity in a large, temperate, heavily modified river, as determined by pyrosequencing

Schultz, Gary E.; Kovatch, Jeffrey J.; Anneken, Emily M.

doi:10.3354/ame01646

Cited by 22 publications

(23 citation statements)

References 41 publications

(72 reference statements)

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“…These data parallel findings in the existing literature in which a consistent freshwater stream microbiome has been proposed (2,9,10,13,19,21,31), though the exact definition of this population and the nomenclature describing this phenomenon have been highly variable. For example, the "core" freshwater community of stream biofilms and sediment was defined by Besemer et al as taxa found in at least 50% of all samples (2).…”

Section: Discussionsupporting

confidence: 84%

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Rapid and Stable Microbial Community Assembly in the Headwaters of a Third-Order Stream

Teachey

McDonald

Ottesen

2019

Appl Environ Microbiol

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Small streams and their headwaters are key sources of microbial diversity in fluvial systems and serve as an entry point for bacteria from surrounding environments. Community assembly processes occurring in these streams shape downstream population structure and nutrient cycles. To elucidate the development and stability of microbial communities along the length of a first-through third-order stream, fine-scale temporal and spatial sampling regimes were employed along Mc-Nutt Creek in Athens, GA, USA. 16S rRNA amplicon libraries were constructed from samples collected on a single day from 19 sites spanning the first 16.76 km of the stream. To provide context for this spatial study and evaluate temporal variability, selected sites at the stream's upper, mid, and lower reaches were sampled daily for 5 days preceding and following the spatial study. In a second study, three sites at and near the creek's headwaters were sampled daily for 11 days to understand initial bacterioplankton community assembly. Both studies revealed decreasing alpha and beta diversity with increasing downstream distance. These trends were accompanied by the enrichment of a small fraction of taxa found at low abundance in headwaterproximal sites. Similar sets of taxa consistently increased in relative abundance in downstream samples over time scales ranging from 1 day to 1 year, many of which belong to clades known to be abundant in freshwater environments. These results underpin the importance of headwaters as the site of rapid in-stream selection that results in the reproducible establishment of a highly stable community of freshwater riverine bacteria. IMPORTANCE Headwater streams are critical introduction points of microbial diversity for larger connecting rivers and play key roles in the establishment of taxa that partake in in-stream nutrient cycling. We examined the microbial community composition of a first-through third-order stream using fine-scale temporal and spatial regimes. Our results show that the bacterioplankton community develops rapidly and predictably from the headwater population with increasing total stream length. Along the length of the stream, the microbial community exhibits substantial diversity loss and enriches repeatedly for select taxa across days and years, although the relative abundances of individual taxa vary over time and space. This repeated enrichment of a stable stream community likely contributes to the stability and flexibility of downstream communities.

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Section: Discussionsupporting

confidence: 84%

“…(21). It is clear that a select and consistent set of taxa dominate freshwater habitats in fluvial systems at all scales (23,25,28,31). However, it is also clear that the abundances of these microbes can vary substantially, both within and between fluvial networks (28).…”

Section: Discussionmentioning

confidence: 99%

Rapid and Stable Microbial Community Assembly in the Headwaters of a Third-Order Stream

Teachey

McDonald

Ottesen

2019

Appl Environ Microbiol

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“…The relative importance of the Proteobacteria decreased significantly from March to April and this shift in total abundance was accompanied by a significant change in the composition of this group. The patterns observed here are consistent with previous studies that found Proteobacteria to be numerically dominant in river and lake habitats when bacterial communities are supported by allochthonous nutrient inputs, and to be less abundant when autochthonous nutrients are most important (Tang et al 2009, Schultz et al 2013. Most notably in March, β-Proteobacteria dominated both filter class communities.…”

Section: Changes In Bacterial Community Composition During Inflow Eventssupporting

confidence: 82%

“…Our knowledge of the ecology of lotic microbes is much less developed than our understanding of marine and lake microbial communities. In particular, there is currently limited knowledge of how microbial communities respond to the constantly shifting environmental conditions that are characteristic of river ecosystems (Curtis & Sloan 2004, Schultz et al 2013.…”

Section: Introductionmentioning

confidence: 99%

River bacterioplankton community responses to a high inflow event

Carney¹,

Mitrovic²,

Jeffries³

et al. 2015

Aquat. Microb. Ecol.

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Microbes drive chemical cycling and productivity within river ecosystems, but their influence may shift when intense allochthonous inputs accompany high freshwater inflow (flood) events. Investigating how floods influence microbial processes is fundamentally important for our understanding of river ecology, but is generally overlooked. We analysed bacterioplankton community composition (BCC) and abundance over 4 mo following an enormous flood event in the Hunter River, Australia, that resulted in a major fish kill. Concentrations of dissolved organic carbon (DOC) and inorganic nutrients (N and P) were up to 3 times higher during the flood event compared to prior and subsequent months. Bacterial cell abundances were up to 10 times higher at impacted sites during the flood event. Using Automated Ribosomal Intergenic Spacer Analysis we found significant shifts in BCC between the flood impacted month and subsequent months (p < 0.05). Distance linear modelling indicated that DOC and dissolved N and P correlated most strongly with BCC patterns during the high inflow, whereas community dynamics correlated most strongly with nitrogen oxides and ammonium during the river's recovery phase. 16S rRNA amplicon pyrosequencing revealed that common soil-associated and facultative anaerobic genera of Proteobacteria were most dominant during the flood period, suggesting that a proportion of the bacterial community observed during this event were potentially inactive soil microbes transported into the river via terrestrial runoff. During the recovery period, Cyanobacteria and freshwater-associated genera of Actinobacteria and Proteobacteria became dominant in 16S rRNA pyrosequencing profiles. These observations indicate that allochthonous nutrients delivered via floods can significantly stimulate bacterial growth, underpinning substrate-controlled succession of bacterial communities and ultimately shaping the ecology within river ecosystems.

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“…The springs of East district was mainly dominated by the bacteria Emticicia (14.83%). Emticicia is a gram-negative bacterial genus belongs to family Cytophagaceae and they are ubiquitous in the aquatic environment (Schultz et al ., 2013; Seo et al ., 2015; Nam et al ., 2016). A number of significant members from the genera were identified in aquatic systems viz.…”

Section: Discussionmentioning

confidence: 99%

First report on Bacterial Diversity of Potable Spring water of Indian Himalayan Region

Singh

et al. 2018

Preprint

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16Water quality of a region directly corroborates with the health index of people. People in the 17 Himalayan hills mainly depend upon the spring water for potability. To determine the microbial 18 ecology of the spring waters of Sikkim, the variable region of 16S rRNA has been sequenced 19 using Illumina MiSeq. Phylum wise annotation showed the East and North district are mostly 20 dominated by Proteobacteria (41% and 35.80%), whereas West and South district is dominated 21 by Planctomycetes (38.46%) and Verrucomicrobia (33%). The consistent dominance phyla in 22 the all the four districts were Bacteriodetes (34-24%) which was highest dominancy in North 23 district and lowest in wets district. Genus wise distribution showed the abundance of Brevifolis, 24 2 Flavobacterium, Verrucomicrobia subdivision3, Emticica, Cytophaga, Prosthecobacter, 25 Planctomycetes, Varivorax, Arcicella, Isosphera, Sedimunibacterium etc. The East district 26 showed highest dominancy of genus Emticicia whereas Planctomycetes in the West district. The 27North district was mainly dominated by genus Arcicella and Brevifollis in the South district. 28North on the antonymous showed totally different sets of microbial diversity. North district 29 showed an abundance of Arcicella, Planctomycetes, Schlerensia and Azohydromonas. The heat 30 map produced by Bray Curtis distance method produced three clusters which showed the close 31 relationship between West and East district microbiome that further related to South district. The 32 sample of North district formed out group that showed different community structure from other 33 three districts. The principle component analysis was showed that the east and South district 34 samples are closely related and distantly correlated to the west Sikkim, but the North district 35 showed completely different microbial community. The canonical correspondence analysis 36 showed correlation between bacterial diversity and hydrochemistry and it was found that the 37 bacterial diversity was influenced by the concentration of different metallic ions like sodium, 38 calcium, barium and iron. This is a first report from the Eastern Himalayan region of India and it 39 largely enhances our knowledge about the microbial structure of potable spring water of Eastern 40 Himalayan. This study is useful for Government of India as well as the state government to adopt 41 the different strategic treatment procedures to improve the quality of water that is supplied to the 42 community resides in the Himalayan regions and solely dependent on this untreated spring water. 43 44 45 46 47 48Microbial communities are the key members of many ecosystems on the earth 49 (Lagkouvardos et al., 2016). The word microbial communities can be described in the terms 50 of richness or evenness as well as composition i.e. abundance of taxa and genes in the sample 51 (Rothschild, 1991). They play a significant role in crucial biological functions ranging from 52 nitrogen and carbon cycles in the environment to regulation of metabolic...

show abstract

Bacterial diversity in a large, temperate, heavily modified river, as determined by pyrosequencing

Cited by 22 publications

References 41 publications

Rapid and Stable Microbial Community Assembly in the Headwaters of a Third-Order Stream

Rapid and Stable Microbial Community Assembly in the Headwaters of a Third-Order Stream

River bacterioplankton community responses to a high inflow event

First report on Bacterial Diversity of Potable Spring water of Indian Himalayan Region

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