Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes

Samad, Sainur; Lee, Hyo‐Jung; Cerbin, Slawek; Meima-Franke, Marion; Bodelier, Paul L. E.

doi:10.3389/fmicb.2020.00582

Cited by 16 publications

(18 citation statements)

References 77 publications

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“…Cyanobacteria were the most abundant and diverse taxonomic group in a set of neutral mine pit lakes in Poland (pH 8) [57]. Actinobacteria (CL500-29 marine group_uncultured bacterium and hgcI clade) co-cycled in microbial planktonic communities in our study lakes; a pattern that has been previously documented in Polish lakes artificially heated with power plant discharge [58], in mesocosms [59], in the Baltic Sea [60], in an Indian brackish lagoon [61], a sewage-affected river in China [62] and a variety of other aquatic habitats both natural and artificial [63][64][65]. It is unclear why these two particular taxa co-dominate assemblages and cycled together over time and did so under such a wide variety of conditions in many different aquatic habitats.…”

Section: Discussionsupporting

confidence: 78%

Aquatic Ecosystems of the Anthropocene: Limnology and Microbial Ecology of Mine Pit Lakes

Blanchette

Lund

2021

Microorganisms

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Mine pit lakes (‘pit lakes’) are new aquatic ecosystems of the Anthropocene. Potentially hundreds of meters deep, these lakes are prominent in the landscape and in the public consciousness. However, the ecology of pit lakes is underrepresented in the literature. The broad goal of this research was to determine the environmental drivers of pelagic microbe assemblages in Australian coal pit lakes. The overall experimental design was four lakes sampled three times, top and bottom, in 2019. Instrument chains were installed in lakes and measurements of in situ water quality and water samples for metals, metalloids, nutrients and microbe assemblage were collected. Lakes were monomictic and the timing of mixing was influenced by high rainfall events. Water quality and microbial assemblages varied significantly across space and time, and most taxa were rare. Lakes were moderately saline and circumneutral; Archeans were not prevalent. Richness also varied by catchment. Microbial assemblages correlated to environmental variables, and no one variable was consistently significant, spatially or temporally. Study lakes were dominated by ‘core’ taxa exhibiting temporal turnover likely driven by geography, water quality and interspecific competition, and the presence of water chemistry associated with an artificial aquifer likely influenced microbial community composition. Pit lakes are deceptively complex aquatic ecosystems that host equally complex pelagic microbial communities. This research established links between microbial assemblages and environmental variables in pit lakes and determined core communities; the first steps towards developing a monitoring program using microbes.

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Section: Discussionsupporting

confidence: 78%

Aquatic Ecosystems of the Anthropocene: Limnology and Microbial Ecology of Mine Pit Lakes

Blanchette

Lund

2021

Microorganisms

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“…Recently published data suggested that similar mechanisms may act in nature where copepods and Daphnia have a lot of their microbiome from the surrounding water (Eckert et al, 2020). Despite this strong seeding from the water, microbiomes of zooplankton are not identical to those of the surrounding water, suggesting that filtering mechanisms do take place in the animals (Eckert et al, 2020; Samad et al, 2020). The diverse data set analysed here in terms of host species from two distantly related phyla (Rotifera and Arthropoda) and in terms of different treatments suggests that the strong environmental effect on the microbiome is a general mechanism for the assembly of the microbial community of freshwater zooplankton.…”

Section: Discussionmentioning

confidence: 99%

Freshwater zooplankton microbiome composition is highly flexible and strongly influenced by the environment

2021

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The association with microbes in plants and animals is known to be beneficial for host's survival and fitness, but the generality of the effect of the microbiome is still debated. For some animals, similarities in microbiome composition reflect taxonomic relatedness of the hosts, a pattern termed phylosymbiosis. The mechanisms behind the pattern could be due to co‐evolution and/or to correlated ecological constraints. General conclusions are hampered by the fact that available knowledge is highly dominated by microbiomes from model species. Here, we addressed the issue of the generality of phylosymbiosis by analysing the species‐specificity of microbiomes across different species of freshwater zooplankton, including rotifers, cladocerans, and copepods, coupling field surveys and experimental manipulations. We found that no signal of phylosymbiosis was present, and that the proportion of “core” microbial taxa, stable and consistent within each species, was very low. Changes in food and temperature under laboratory experimental settings revealed that the microbiome of freshwater zooplankton is highly flexible and can be influenced by the external environment. Thus, the role of co‐evolution, strict association, and interaction with microbes within the holobiont concept highlighted for vertebrates, corals, sponges, and other animals does not seem to be supported for all animals, at least not for freshwater zooplankton. Zooplankton floats in the environment where both food and bacteria that can provide help in digesting such food are available. In addition, there is probably redundancy for beneficial bacterial functions in the environment, not allowing a strict host‐microbiome association to originate and persist.

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“…In freshwater environments worldwide, Actinobacteria are ubiquitous and highly abundant ( Newton et al, 2011 ; Samad et al, 2020 ). However, Actinobacteria never dominate Daphnia microbiome, although Nocardioidaceae and Microbacteriaceae are often present ( Qi et al, 2009 ; Eckert et al, 2016 ; Callens et al, 2018 ; Mushegian et al, 2018 ; Cooper and Cressler, 2020 ; Motiei et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Understanding Biofilm Formation in Ecotoxicological Assays With Natural and Anthropogenic Particulates

2021

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Fossil-made polymers harbor unique bacterial assemblages, and concerns have been raised that ingested microplastic may affect the consumer gut microbiota and spread pathogens in animal populations. We hypothesized that in an ecotoxicity assay with a mixture of polystyrene (PS) and clay: (1) microbiome of the test animals inoculates the system with bacteria; (2) relative contribution of PS and the total amount of suspended solids (SS) select for specific bacterial communities; and (3) particle aggregation is affected by biofilm community composition, with concomitant effects on the animal survival. Mixtures of PS and clay at different concentrations of SS (10, 100, and 1000 mg/L) with a varying microplastics contribution (%PS; 0–80%) were incubated with Daphnia magna, whose microbiome served as an inoculum for the biofilms during the exposure. After 4-days of exposure, we examined the biofilm communities by 16S rRNA gene sequencing, particle size distribution, and animal survival. The biofilm communities were significantly different from the Daphnia microbiota used to inoculate the system, with an overrepresentation of predatory, rare, and potentially pathogenic taxa in the biofilms. The biofilm diversity was stimulated by %PS and decreased by predatory bacteria. Particle aggregate size and the biofilm composition were the primary drivers of animal survival, with small particles and predatory bacteria associated with a higher death rate. Thus, in effect studies with solid waste materials, ecological interactions in the biofilm can affect particle aggregation and support potentially harmful microorganisms with concomitant effects on the test animals.

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Niche Differentiation of Host-Associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes

Cited by 16 publications

References 77 publications

Aquatic Ecosystems of the Anthropocene: Limnology and Microbial Ecology of Mine Pit Lakes

Aquatic Ecosystems of the Anthropocene: Limnology and Microbial Ecology of Mine Pit Lakes

Freshwater zooplankton microbiome composition is highly flexible and strongly influenced by the environment

Understanding Biofilm Formation in Ecotoxicological Assays With Natural and Anthropogenic Particulates

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