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

Changes in the abundance and diversity of bacterial and archaeal communities at different depths in a eutrophic freshwater lake in southwestern Mexico

Bacteria and archaea play a fundamental role in the biogeochemical cycles of organic matter, pollutants, and nutrients to maintain the trophic state of aquatic ecosystems. However, very little is known about the composition patterns of microbial communities in vertical distribution (water column) in freshwater lakes and their relationship with the physicochemical properties of water. "La Encantada" lake in the Lagunas de Montebello National Park (LMNP) is a site of interest due to the anthropogenic impact received and the little information about it. In this study, 3 sites were evaluated; samples were collected using 0-15 m deep water columns and analyzed using Illumina MiSeq sequencing technology based on the 16S rRNA gene. The physical parameters of pH, temperature, dissolved oxygen, electrolytic conductivity, and PO-4 were determined. The results revealed clear differences in the microbial composition of the water throughout the column; the most abundant phyla in bacterial communities were Proteobacteria (23.2%), Cyanobacteria (17.3%), and Bacteroidetes (17.2%), and for archaea were Crenarchaeota (35.9%) and Euryarchaeota (33.2%). PICRUSt metabolic inference analysis revealed that the main functional genes were related to cellular processes and biodegradation of xenobiotics, indicating an increasing trend of contaminants and residual discharges that may act as a precursor to alter microbial communities and stability of the lakes. At depths of 10 and 15 m, the microbial diversity was greater; likewise, the correlation between the physicochemical parameters and the microbial communities at the genus level showed that Chlorobaculum, Desulfomonile, and Candidatus Xiphinematobacter were favored by an increase in dissolved phosphates and by the decrease in pH and temperature. These results highlight that the microbial communities exhibit variation in their composition due to the effect of depth and physicochemical parameters, which could play a role as biological factors in the trophic states of a lake.

Diversity assessment of photosynthesizers: comparative analysis of pre-cultivated and natural microbiome of sediments from Cerrado biome in Maranhão, Brazil

Photosynthetic microorganisms are important components of most ecosystems and have important roles regarding biogeochemical cycles and the basis of the trophic chain. However, they sometimes are present in low abundance compared to other heterotrophic organisms. The Chapada das Mesas National Park (PNCM) is a Conservation Unit in Brazilian Cerrado biome, which is considered a hotspot for biodiversity conservation and possesses important rivers, waterfalls, and springs with economical and touristic importance. The aim of this study was to perform a comparative analysis of enriched and total microbiome of sediments to understand the impact of pre-cultivation in discovery of underrepresented groups like photosynthesizers. All sediment samples were cultivated in BG-11 medium under illumination to enrich for photosynthetic microorganisms and both the raw samples and the enriched ones were submitted to DNA extraction and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene on the Ion Torrent platform. The reads were analyzed using QIIME2 software and the Phyloseq package. The enrichment allowed detection and identification of many genera of cyanobacteria in the Chapada das Mesas National Park (PNCM), which would probably not be possible without the combination of approaches. A total of 58 groups of photosynthetic microorganisms were classified in the samples from the enrichments and their relative abundance based on amplified 16S rRNA sequences were estimated, highlighting the genus Synechocystis which represented 10.10% of the abundance of the phylum Cyanobacteria and the genus Dunaliella, which represented 45.66% of the abundance of algae as the most abundant groups at the PNCM. In the enrichments, microorganisms from the phyla Proteobacteria (45.2%), Bacteroidetes (18%), and Planctomycetes (3.3%) were also identified, since there are ecological associations between the photosynthetic community and other groups of heterotrophic microorganisms. As for the functional analysis, metabolic functions associated with methanotrophy and methylotrophy, hydrocarbon degradation, phototrophy, and nitrogen fixation were predicted. The results highlight a great diversity of photosynthetic microorganisms in Cerrado and the importance of using a combination of approaches when analyzing target groups which are usually underrepresented such as cyanobacteria and microalgae.

Methane-Derived Carbon as a Driver for Cyanobacterial Growth

Methane, a potent greenhouse gas produced in freshwater ecosystems, can be used by methane-oxidizing bacteria (MOB) and can therefore subsidize the pelagic food web with energy and carbon. Consortia of MOB and photoautotrophs have been described in aquatic ecosystems and MOB can benefit from photoautotrophs which produce oxygen, thereby enhancing CH₄ oxidation. Methane oxidation can account for accumulation of inorganic carbon (i.e., CO₂) and the release of exometabolites that may both be important factors influencing the structure of phytoplankton communities. The consortium of MOB and phototroph has been mainly studied for methane-removing biotechnologies, but there is still little information on the role of these interactions in freshwater ecosystems especially in the context of cyanobacterial growth and bloom development. We hypothesized that MOB could be an alternative C source to support cyanobacterial growth in freshwater systems. We detected low δ¹³C values in cyanobacterial blooms (the lowest detected value −59.97‰ for Planktothrix rubescens) what could be the result of the use of methane-derived carbon by cyanobacteria and/or MOB attached to their cells. We further proved the presence of metabolically active MOB on cyanobacterial filaments using the fluorescein isothiocyanate (FITC) based activity assay. The PCR results also proved the presence of the pmoA gene in several non-axenic cultures of cyanobacteria. Finally, experiments comprising the co-culture of the cyanobacterium Aphanizomenon gracile with the methanotroph Methylosinus sporium proved that cyanobacterial growth was significantly improved in the presence of MOB, presumably through utilizing CO₂ released by MOB. On the other hand, ¹³C-CH₄ labeled incubations showed the uptake and assimilation of MOB-derived metabolites by the cyanobacterium. We also observed a higher growth of MOB in the presence of cyanobacteria under a higher irradiance regime, then when grown alone, underpinning the bidirectional influence with as of yet unknown environmental consequences.

Host Dependence of Zooplankton-Associated Microbes and Their Ecological Implications in Freshwater Lakes

Zooplankton is colonized by quite different microbes compared with free-living and particle-associated bacteria, serving as a non-negligible niche of bacteria in aquatic ecosystems. Yet detailed analysis of these bacterial groups is still less known, especially in freshwater lakes. To widen our knowledge of host-microbe interaction and bacterial ecosystem functions, we chose two specific populations of zooplankton, i.e., cladoceran Moina and copepod Calanoids, as hosts from five natural lakes, and illustrated detailed features of their associated bacteria. Through 16S rRNA gene sequencing, we found microbes colonized on Calanoids presented significantly higher α-diversity, stronger bacterial interaction and metabolic function potentials than for Moina. It was also notable that zooplankton-associated bacteria showed a high potential of fatty acid metabolism, which is beneficial for host’s development. Moreover, we found that zooplankton-associated microbes may exert profound effects on biogeochemical cycles in freshwater lakes, since several bacterial members able to participate in carbon and nitrogen cycles were found abundant. Overall, our study expands current understanding of the host-microbe interaction and underlying ecological dynamics in freshwater ecosystem.

Temperature differently affected methanogenic pathways and microbial communities in sub-Antarctic freshwater ecosystems

Freshwater ecosystems are responsible for an important part of the methane (CH₄) emissions which are likely to change with global warming. This study aims to evaluate temperature-induced (from 5 to 20 °C) changes on microbial community structure and methanogenic pathways in five sub-Antarctic lake sediments from Magallanes strait to Cape Horn, Chile. We combined in situ CH₄ flux measurements, CH₄ production rates (MPRs), gene abundance quantification and microbial community structure analysis (metabarcoding of the 16S rRNA gene). Under unamended conditions, a temperature increase of 5 °C doubled MPR while microbial community structure was not affected. Stimulation of methanogenesis by methanogenic precursors as acetate and H₂/CO₂, resulted in an increase of MPRs up to 127-fold and 19-fold, respectively, as well as an enrichment of mcrA-carriers strikingly stronger under acetate amendment. At low temperatures, H₂/CO₂-derived MPRs were considerably lower (down to 160-fold lower) than the acetate-derived MPRs, but the contribution of hydrogenotrophic methanogenesis increased with temperature. Temperature dependence of MPRs was significantly higher in incubations spiked with H₂/CO₂ (c. 1.9 eV) compared to incubations spiked with acetate or unamended (c. 0.8 eV). Temperature was not found to shape the total microbial community structure, that rather exhibited a site-specific variability among the studied lakes. However, the methanogenic archaeal community structure was driven by amended methanogenic precursors with a dominance of Methanobacterium in H₂/CO₂-based incubations and Methanosarcina in acetate-based incubations. We also suggested the importance of acetogenic H₂-production outcompeting hydrogenotrohic methanogenesis especially at low temperatures, further supported by homoacetogen proportion in the microcosm communities. The combination of in situ-, and laboratory-based measurements and molecular approaches indicates that the hydrogenotrophic pathway may become more important with increasing temperatures than the acetoclastic pathway. In a continuously warming environment driven by climate change, such issues are crucial and may receive more attention.

Understanding Biofilm Formation in Ecotoxicological Assays With Natural and Anthropogenic Particulates

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.

Parasites, pathogens, and other symbionts of copepods

There is a large diversity of eukaryotic symbionts of copepods, dominated by epizootic protists such as ciliates, and metazoan parasites. Eukaryotic endoparasites, copepod-associated bacteria, and viruses are less well known, partly due to technical limitations. However, new molecular techniques, combined with a range of other approaches, provide a complementary toolkit for understanding the complete symbiome of copepods and how the symbiome relates to their ecological roles, relationships with other biota, and responses to environmental change. In this review we provide the most complete overview of the copepod symbiome to date, including microeukaryotes, metazoan parasites, bacteria, and viruses, and provide extensive literature databases to inform future studies.

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

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.

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

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.

Leeia aquatica sp. nov., isolated from freshwater

A Gram-stain-negative, rod-shaped, obligately aerobic, motile by a single polar flagellum, chemoheterotrophic bacterium, designated strain IMCC25680^T, was isolated from surface water in Chungju Lake, Republic of Korea. 16S rRNA gene sequence analysis revealed that strain IMCC25680^T was most closely related to Leeia oryzae HW7^T with 95.5% sequence similarity and formed a robust clade with L. oryzae HW7^T. Whole genome sequencing showed that strain IMCC25680^T had a genome 3.6 Mbp long with 60.7 mol% DNA G+C content. Average nucleotide identity and digital DNA-DNA hybridization values between strain IMCC25680^T and L. oryzae HW7^T were 72.4% and 18.5%, respectively, indicating that the novel strain represents a novel species of the genus Leeia. The major cellular fatty acids of strain IMCC25680^T were iso-C_16:0 and summed feature 3 (comprising C_16:1 ω6c and/or C_16:1 ω7c). The respiratory quinone detected in the strain was ubiquinone-8. The major polar lipids were found to be phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and two unidentified polar lipids. On the basis of the phylogenetic and phenotypic characterization, strain IMCC25680^T was considered to represent a novel species within the genus Leeia, for which the name Leeia aquatica sp. nov. is proposed. The type strain is IMCC25680^T (=KACC 19487^T =NBRC 113132^T).