Dispersal Modifies the Diversity and Composition of Active Bacterial Communities in Response to a Salinity Disturbance

Shen, Dandan; Langenheder, Silke; Jürgens, Klaus

doi:10.3389/fmicb.2018.02188

Cited by 53 publications

(46 citation statements)

References 60 publications

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“…Water column freshwater microbial taxa are particularly sensitive to the salt stress imposed by brackish conditions (Burke and Baird , Ewert and Deming ), whereas marine microbial taxa are more robust to brackish waters, because of wider salinity tolerance (Herlemann et al ). Compositional turnover is high for water (Kisand et al , Shen et al ) and soil (Dang et al ) microbial communities during brackish exposure, and we expect similar turnover of the water column community with this strong environmental filter. However, the impact of novel biotic interactions from a community blending freshwater and marine microbiomes is unknown.…”

Section: Introductionmentioning

confidence: 70%

Rare microbial taxa emerge when communities collide: freshwater and marine microbiome responses to experimental mixing

Rocca

Simonin

Bernhardt

et al. 2020

Ecology

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Whole microbial communities regularly merge with one another, often in tandem with their environments, in a process called community coalescence. Such events impose substantial changes: abiotic perturbation from environmental blending and biotic perturbation of community merging. We used an aquatic mixing experiment to unravel the effects of these perturbations on the whole microbiome response and on the success of individual taxa when distinct freshwater and marine communities coalesce. We found that an equal mix of freshwater and marine habitats and blended microbiomes resulted in strong convergence of the community structure toward that of the marine microbiome. The enzymatic potential of these blended microbiomes in mixed media also converged toward that of the marine, with strong correlations between the multivariate response patterns of the enzymes and of community structure. Exposing each endmember inocula to an axenic equal mix of their freshwater and marine source waters led to a 96% loss of taxa from our freshwater microbiomes and a 66% loss from our marine microbiomes. When both inocula were added together to this mixed environment, interactions amongst the communities led to a further loss of 29% and 49% of freshwater and marine taxa, respectively. Under both the axenic and competitive scenarios, the diversity lost was somewhat counterbalanced by increased abundance of microbial taxa that were too rare to detect in the initial inocula. Our study emphasizes the importance of the rare biosphere as a critical component of microbial community responses to community coalescence.

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Section: Introductionmentioning

confidence: 70%

Rare microbial taxa emerge when communities collide: freshwater and marine microbiome responses to experimental mixing

Rocca

Simonin

Bernhardt

et al. 2020

Ecology

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“…In contrast, Pelagibacterales, the SAR86 clade, and Puniceispirillales, which were abundant in the SOLA initial community, were generally underrepresented in the resuscitated communities, particularly those grown in ASW with DOM supplements. This is not surprising as representatives of the order Pelagibacterales are notoriously hard to grow under laboratory conditions (e.g., Sharma et al, 2013 ; Shen et al, 2018b ). Nevertheless, members of the Pelagibacterales were actively growing, particularly in the F-SEA medium, as supported by higher cell abundances during the final incubation day compared to the incubation start ( Figure 6C ; positive log2-fold changes, p adj < 0.1).…”

Section: Discussionmentioning

confidence: 99%

Cryopreservation and Resuscitation of Natural Aquatic Prokaryotic Communities

2021

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Experimental reproducibility in aquatic microbial ecology is critical to predict the dynamics of microbial communities. However, controlling the initial composition of naturally occurring microbial communities that will be used as the inoculum in experimental setups is challenging, because a proper method for the preservation of those communities is lacking. To provide a feasible method for preservation and resuscitation of natural aquatic prokaryote assemblages, we developed a cryopreservation procedure applied to natural aquatic prokaryotic communities. We studied the impact of inoculum size, processing time, and storage time on the success of resuscitation. We further assessed the effect of different growth media supplemented with dissolved organic matter (DOM) prepared from naturally occurring microorganisms on the recovery of the initially cryopreserved communities obtained from two sites that have contrasting trophic status and environmental heterogeneity. Our results demonstrated that the variability of the resuscitation process among replicates decreased with increasing inoculum size. The degree of similarity between initial and resuscitated communities was influenced by both the growth medium and origin of the community. We further demonstrated that depending on the inoculum source, 45–72% of the abundant species in the initially natural microbial communities could be detected as viable cells after cryopreservation. Processing time and long-term storage up to 12 months did not significantly influence the community composition after resuscitation. However, based on our results, we recommend keeping handling time to a minimum and ensure identical incubation conditions for repeated resuscitations from cryo-preserved aliquots at different time points. Given our results, we recommend cryopreservation as a promising tool to advance experimental research in the field of microbial ecology.

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“…Hence, the extent of salinity intrusion may also result in the loss of diversity and richness of the microbial communities (Shen et al, 2018) in the Rajang River.…”

Section: Possible Pathogenic Bacteria And/or Anthropogenic Influence mentioning

confidence: 99%

Biogeographical distribution of Microbial Communities along the Rajang River-South China Sea Continuum

Sia¹,

Zhu²,

Zhang³

et al. 2019

Preprint

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Abstract. Microbial community composition and diversity in freshwater habitats, especially in lotic environments, are much less studied compared to marine and soil communities. The Rajang River is the main drainage system for central Sarawak in Malaysian Borneo and passes through peat domes whereby peat-rich material is being fed into the system and eventually into the southern South China Sea. Microbial communities found within peat-rich systems are important biogeochemical cyclers in terms of methane and carbon dioxide sequestration. To address the critical lack of knowledge about microbial communities in tropical (peat-draining) rivers, this study represents the first seasonal assessment targeted at establishing a foundational understanding of the microbial communities of the Rajang River-South China Sea continuum. This was carried out utilizing 16S rRNA gene amplicon sequencing via Illumina MiSeq in size-fractionated samples (0.2 and 3.0 μm GF/C filter membranes) covering different biogeographical features/sources from headwaters to coastal waters. The microbial communities found along the Rajang river exhibited taxa common to rivers (i.e. the predominance of β-Proteobacteria) while estuarine and marine regions exhibited taxa that were common to the aforementioned regions as well (i.e. predominance of α- and γ-Proteobacteria). This is in agreement with studies from other rivers which observed similar changes along the salinity gradients. In terms of particulate versus free-living bacteria, nonmetric multi-dimensional scaling (NMDS) results showed similarly distributed microbial communities with varying separation between seasons. Distinct patterns were observed based on linear models as a result of the changes in salinity along with variation of other biogeochemical parameters. Alpha diversity indices indicated that microbial communities were higher in diversity upstream compared to the marine and estuarine regions whereas anthropogenic perturbations led to increased richness but less diversity. Despite the observed changes in bacterial community composition and diversity that occur along the Rajang River to sea continuum, the PICRUST predictions showed minor variations. The results provide essential context for future studies such as further analyses on the ecosystem health in response to anthropogenic land-use practices and probable development of biomarkers to improve the monitoring of water quality in this region.

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Dispersal Modifies the Diversity and Composition of Active Bacterial Communities in Response to a Salinity Disturbance

Cited by 53 publications

References 60 publications

Rare microbial taxa emerge when communities collide: freshwater and marine microbiome responses to experimental mixing

Rare microbial taxa emerge when communities collide: freshwater and marine microbiome responses to experimental mixing

Cryopreservation and Resuscitation of Natural Aquatic Prokaryotic Communities

Biogeographical distribution of Microbial Communities along the Rajang River-South China Sea Continuum

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