Sediment bacteria in an urban stream: Spatiotemporal patterns in community composition

Roberto, Alescia A.; Gray, Jonathon B. Van; Leff, Laura Gunn

doi:10.1016/j.watres.2018.01.045

Cited by 85 publications

(60 citation statements)

References 158 publications

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“…The bacterial community structure shifted with increasing urban land cover but with no impacts on alpha diversity assessed through relative diversity indices (OTU richness, Shannon index, evenness), as previously observed in other studies (Lear et al, ; Zeglin, ; Roberto et al, ). These results are in contrast with widely reported decreases in the diversity of ciliate, macroinvertebrate and fish communities in urban streams (Helms et al, ; Moore and Palmer, ; Lear et al, ).…”

Section: Discussionsupporting

confidence: 81%

“…The positive responders were broadly distributed throughout the bacterial phylogeny with members of the family Comamonadaceae (Betaproteobacteria) including the highest number of tolerant indicator taxa (14% of OTUs in this family). Previous studies have reported taxa belonging to the Comamonadaceae family were dominant in urban streams in Ohio, USA, and in India (Jani et al, 2018;Roberto et al, 2018). Many members of the Comamonadaceae exhibit copiotrophic lifestyles and are stimulated by nutrient pollution (Yu et al, 2017).…”

Section: Identification Of Promising Bacterial Indicator Taxa To Infementioning

confidence: 99%

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In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient

Simonin

Voss

Hassett

et al. 2019

Environmental Microbiology

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Summary A majority of environmental studies describe microbiomes at coarse scales of taxonomic resolution (bacterial community, phylum), ignoring key ecological knowledge gained from finer‐scales and microbial indicator taxa. Here, we characterized the distribution of 940 bacterial taxa from 41 streams along an urbanization gradient (0%–83% developed watershed area) in the Raleigh‐Durham area of North Carolina (USA). Using statistical approaches derived from macro‐organismal ecology, we found that more bacterial taxa were classified as intolerant than as tolerant to increasing watershed urbanization (143 vs 48 OTUs), and we identified a threshold of 12.1% developed watershed area beyond which the majority of intolerant taxa were lost from streams. Two bacterial families strongly decreased with urbanization: Acidobacteriaceae (Acidobacteria) and Xanthobacteraceae (Alphaproteobacteria). Tolerant taxa were broadly distributed throughout the bacterial phylogeny, with members of the Comamonadaceae family (Betaproteobacteria) presenting the highest number of tolerant taxa. Shifts in microbial community structure were strongly correlated with a stream biotic index, based on macroinvertebrate composition, suggesting that microbial assemblages could be used to establish biotic criteria for monitoring aquatic ecosystems. In addition, our study shows that classic methods in community ecology can be applied to microbiome datasets to identify reliable microbial indicator taxa and determine the environmental constraints on individual taxa distributions along environmental gradients.

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Section: Discussionsupporting

confidence: 81%

Section: Identification Of Promising Bacterial Indicator Taxa To Infementioning

confidence: 99%

In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient

Simonin

Voss

Hassett

et al. 2019

Environmental Microbiology

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“…Usually RT and CART showed weak competition capability and low growth rate (Campbell et al, 2011;Logares et al, 2015), whereas AT can compete for more substrates and well adapt to an ecosystem via active growth and proliferation in a wide niche (Pedrós-Alió, 2006;Jousset et al, 2017;Xue et al, 2018). This suggests that the composition of microbial communities is strongly affected by environmentally induced species sorting (Roberto et al, 2018). Therefore, taxa with various abundances in bacterial communities from SP were impacted by unequal environmental filtering.…”

Section: Environmental Factors Shaping Bacterial Communitiesmentioning

confidence: 99%

Rare Species Shift the Structure of Bacterial Communities Across Sphagnum Compartments in a Subalpine Peatland

Xiao

Evers

et al. 2020

Front. Microbiol.

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Sphagnum-associated microbiomes are crucial to Sphagnum growth and peatland ecological functions. However, roles of rare species in bacterial communities across Sphagnum compartments are poorly understood. Here the structures of rare taxa (RT) and conditionally abundant and rare taxa (CART) from Sphagnum palustre peat (SP), S. palustre ectosphere (Ecto) and S. palustre endosphere (Endo) were investigated in the Dajiuhu Peatland, central China. Our results showed that plant compartment effects significantly altered the diversities and structures of bacterial communities. The Observed species and Simpson indices of RT and CART in alpha diversity significantly increased from Endo to SP, with those of Ecto in-between. The variations of community dissimilarities of RT and CART among compartments were consistent with those of whole bacterial communities (WBC). Network analysis indicated a nonrandom co-occurrence pattern of WBC and all keystone species are affiliated with RT and CART, indicating their important role in sustaining the WBC. Furthermore, the community structures of RT and CART in SP were significantly shaped by water table and total nitrogen content, which coincided with the correlations between WBC and environmental factors. Collectively, our results for the first time confirm the importance of rare species to bacterial communities through structural and predicted functional analyses, which expands our understanding of rare species in Sphagnum-associated microbial communities in subalpine peatlands.

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“…This is not straightforward when using 16S rRNA amplicon approaches, however, we attempted to predict the potential functional genes associated with rhizosphere, bulk soil, and root endosphere microbiomes based on the presence of bacterial OTUs. The major KEGG pathways in our study, Metabolism, Genetic Information Processing, and Environmental Information Processing, were also the major pathways in flooded paddy soil and sediment (Xiao et al, 2017;Roberto et al, 2018). Under different irrigation water sources, lipid metabolism and carbohydrate metabolisms decreased in rhizosphere and bulk soil with biochar supplementation (Table S5) The selectivity of roots for the rhizosphere soil microbiome resulted in higher abundance of putative PGPR in rhizosphere soil (Yang et al, 2017), but different water quality irrigation and biochar supplementation had various effects upon specific PGPR.…”

Section: Effects Of Coupled Biochar Supplementation and Irrigation Wamentioning

confidence: 63%

Variations in soil and plant-microbiome composition with different quality irrigation waters and biochar supplementation

Cui

Fan

et al. 2019

Applied Soil Ecology

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Sediment bacteria in an urban stream: Spatiotemporal patterns in community composition

Cited by 85 publications

References 158 publications

In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient

In search of microbial indicator taxa: shifts in stream bacterial communities along an urbanization gradient

Rare Species Shift the Structure of Bacterial Communities Across Sphagnum Compartments in a Subalpine Peatland

Variations in soil and plant-microbiome composition with different quality irrigation waters and biochar supplementation

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