Taxonomic and functional diversity provides insight into microbial pathways and stress responses in the saline Qinghai Lake, China

Network Analysis Indicates Microbial Assemblage Differences in Life Stages of Cladophora

Cladophora represents a microscopic forest that provides many ecological niches and fosters a diverse microbiota. However, the microbial community on Cladophora in brackish lakes is still poorly understood. In this study, the epiphytic bacterial communities of Cladophora in Qinghai Lake were investigated at three life stages (attached, floating, and decomposing). We found that in the attached stage, Cladophora was enriched with chemoheterotrophic and aerobic microorganisms, including Yoonia-Loktanella and Granulosicoccus. The proportion of phototrophic bacteria was higher in the floating stage, especially Cyanobacteria. The decomposing stage fostered an abundance of bacteria that showed vertical heterogeneity from the surface to the bottom. The surface layer of Cladophora contained mainly stress-tolerant chemoheterotrophic and photoheterotrophic bacteria, including Porphyrobacter and Nonlabens. The microbial community in the middle layer was similar to that of floating-stage Cladophora. Purple oxidizing bacteria were enriched in the bottom layer, with Candidatus Chloroploca, Allochromatium, and Thiocapsa as the dominant genera. The Shannon and Chao1 indices of epibiotic bacterial communities increased monotonically from the attached stage to the decomposing stage. Microbial community composition and functional predictions indicate that a large number of sulfur cycle-associated bacteria play an important role in the development of Cladophora. These results suggest that the microbial assemblage on Cladophora in a brackish lake is complex and contributes to the cycling of materials. IMPORTANCE Cladophora represents a microscopic forest that provides many ecological niches fostering a diverse microbiota, with a complex and intimate relationship between Cladophora and bacteria. Many studies have focused on the microbiology of freshwater Cladophora, but the composition and succession of microorganisms in different life stages of Cladophora, especially in brackish water, have not been explored. In this study, we investigated the microbial assemblages in the life stages of Cladophora in the brackish Qinghai Lake. We show that heterotrophic and photosynthetic autotrophic bacteria are enriched in attached and floating Cladophora, respectively, whereas the epiphytic bacterial community shows vertical heterogeneity in decomposing mats.

The Effect of Spring Water Geochemistry on Copper Proteins in Tengchong Hot Springs, China

Copper (Cu) is an essential trace metal cofactor for a variety of proteins; however, excess Cu is toxic to most organisms. Cu homeostasis is maintained by a complex machinery of Cu binding proteins that control the uptake, transport, sequestration, and efflux of Cu ions. Despite the importance of Cu binding proteins in electron transfer, substrate oxidation, superoxide dismutation, and denitrification, little information exists about microbial Cu utilization in extreme environments, where the geochemical conditions may affect Cu bioavailability. Using metagenomic data from 9 hot springs in Tengchong, China, which range in temperature from 42°C to 96°C and in pH from 2.3 to 9, the effects of pH, temperature, and spring geochemistry on the distribution of Cu binding domains of proteins and oxidoreductases were studied. Dissolved Cu and Cu binding domains were detected across all temperature and pH gradients. Cu binding domains of cytochrome c oxidase subunits, heavy-metal-associated domains, and nitrous oxide reductase were detected at all sites. DoxB, a quinol oxidase, and other quinol oxidase subunits were the dominant Cu binding oxidoreductase subunits present at low-pH and high-temperature sites, whereas cbb ₃-type cytochrome c oxidase subunits were dominant at high-pH and high-temperature sites. Additionally, aa ₃-type cytochrome c oxidase was more prominent than cbb ₃-type cytochrome c oxidase under circumneutral-pH conditions. This suggests that the type of cytochrome c oxidase pathway and the Cu proteins employed by microbes to carry out important functions such as energy acquisition and efflux of excess Cu are affected by the physicochemical conditions of the springs.IMPORTANCE Copper is present in a variety of proteins and is required to carry out essential functions by all organisms. However, in hot spring environments, copper availability may be limited due to the high temperatures and the wide range in pH. The significance of our research is in relating the physicochemical environment to the distribution of copper proteins across hot spring environments, which provides increased understanding of primary functions and adaptions in these environments.

Microbial functional diversity: From concepts to applications

Functional diversity is increasingly recognized by microbial ecologists as the essential link between biodiversity patterns and ecosystem functioning, determining the trophic relationships and interactions between microorganisms, their participation in biogeochemical cycles, and their responses to environmental changes. Consequently, its definition and quantification have practical and theoretical implications. In this opinion paper, we present a synthesis on the concept of microbial functional diversity from its definition to its application. Initially, we revisit to the original definition of functional diversity, highlighting two fundamental aspects, the ecological unit under study and the functional traits used to characterize it. Then, we discuss how the particularities of the microbial world disallow the direct application of the concepts and tools developed for macroorganisms. Next, we provide a synthesis of the literature on the types of ecological units and functional traits available in microbial functional ecology. We also provide a list of more than 400 traits covering a wide array of environmentally relevant functions. Lastly, we provide examples of the use of functional diversity in microbial systems based on the different units and traits discussed herein. It is our hope that this paper will stimulate discussions and help the growing field of microbial functional ecology to realize a potential that thus far has only been attained in macrobial ecology.

Abundance and taxonomic affiliation of molybdenum transport and utilization genes in Tengchong hot springs, China

The nitrogen, sulfur and carbon cycles all rely on critical microbial transformations that are carried out by enzymes that require molybdenum (Mo) as a cofactor. Despite Mo importance in these biogeochemical cycles, little information exists about microbial Mo utilization in extreme environments where, due to geochemical conditions, bioavailable Mo may be limited. Using metagenomic data from nine hot springs in Tengchong, Yunnan Province, China, which range in temperature from 42°C to 96°C and pH from 2.3 to 9, the effects of pH, temperature and spring geochemistry on the abundance and taxonomic affiliation of genes related to Mo were studied. Dissolved Mo was only detected at sites with circumneutral pH. However, processes and organisms that require Mo were detected at all sites across all temperature and pH gradients. All sites contained xanthine dehydrogenase, formate dehydrogenase, carbon-monoxide dehydrogenase, nitrate reductase, sulfite oxidase and methionine-sulfoxide reductase despite different community compositions. This suggests that different microbial communities, resulting from different physicochemical conditions, may be performing similar metabolic functions. Furthermore, the abundance and taxonomic diversity of Mo-related annotations increased with higher concentrations of Mo. This study shows that despite geochemical conditions that can limit Mo bioavailability, microbes require Mo for a variety of processes.

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams

Understanding microbial communities in terms of taxon and function is essential to decipher the biogeochemical cycling in aquatic ecosystems. Lakes and their input streams are highly linked. However, the differences between microbial assemblages in streams and lakes are still unclear. In this study, we conducted an intensive field sampling of microbial communities from lake water and stream biofilms in the Qinghai Lake watershed, the largest lake in China. We determined bacterial communities using high-throughput 16S rRNA gene sequencing and predicted functional profiles using PICRUSt to determine the taxonomic and functional differences between microbial communities in stream biofilms and lake water. The results showed that stream biofilms and lake water harbored distinct microbial communities. The microbial communities were different taxonomically and functionally between stream and lake. Moreover, streams biofilms had a microbial network with higher connectivity and modularity than lake water. Functional beta diversity was strongly correlated with taxonomic beta diversity in both the stream and lake microbial communities. Lake microbial assemblages displayed greater predicted metabolic potentials of many metabolism pathways while the microbial assemblages in stream biofilms were more abundant in xenobiotic biodegradation and metabolism and lipid metabolism. Furthermore, lake microbial assemblages had stronger predicted metabolic potentials in amino acid metabolism, carbon fixation, and photosynthesis while stream microbial assemblages were higher in carbohydrate metabolism, oxidative phosphorylation, and nitrogen metabolism. This study adds to our knowledge of stream-lake linkages from the functional and taxonomic composition of microbial assemblages.

Bacterial community structure and function shift along a successional series of tidal flats in the Yellow River Delta

Coastal ecosystems play significant ecological and economic roles but are threatened and facing decline. Microbes drive various biogeochemical processes in coastal ecosystems. Tidal flats are critical components of coastal ecosystems; however, the structure and function of microbial communities in tidal flats are poorly understood. Here we investigated the seasonal variations of bacterial communities along a tidal flat series (subtidal, intertidal and supratidal flats) and the factors affecting the variations. Bacterial community composition and diversity were analyzed over four seasons by 16S rRNA genes using the Ion Torrent PGM platform. Bacterial community composition differed significantly along the tidal flat series. Bacterial phylogenetic diversity increased while phylogenetic turnover decreased from subtidal to supratidal flats. Moreover, the bacterial community structure differed seasonally. Canonical correspondence analysis identified salinity as a major environmental factor structuring the microbial community in the sediment along the successional series. Meanwhile, temperature and nitrite concentration were major drivers of seasonal microbial changes. Despite major compositional shifts, nitrogen, methane and energy metabolisms predicted by PICRUSt were inhibited in the winter. Taken together, this study indicates that bacterial community structure changed along the successional tidal flat series and provides new insights on the characteristics of bacterial communities in coastal ecosystems.

The transcriptional response of microbial communities in thawing Alaskan permafrost soils

Thawing of permafrost soils is expected to stimulate microbial decomposition and respiration of sequestered carbon. This could, in turn, increase atmospheric concentrations of greenhouse gasses, such as carbon dioxide and methane, and create a positive feedback to climate warming. Recent metagenomic studies suggest that permafrost has a large metabolic potential for carbon processing, including pathways for fermentation and methanogenesis. Here, we performed a pilot study using ultrahigh throughput Illumina HiSeq sequencing of reverse transcribed messenger RNA to obtain a detailed overview of active metabolic pathways and responsible organisms in up to 70 cm deep permafrost soils at a moist acidic tundra location in Arctic Alaska. The transcriptional response of the permafrost microbial community was compared before and after 11 days of thaw. In general, the transcriptional profile under frozen conditions suggests a dominance of stress responses, survival strategies, and maintenance processes, whereas upon thaw a rapid enzymatic response to decomposing soil organic matter (SOM) was observed. Bacteroidetes, Firmicutes, ascomycete fungi, and methanogens were responsible for largest transcriptional response upon thaw. Transcripts indicative of heterotrophic methanogenic pathways utilizing acetate, methanol, and methylamine were found predominantly in the permafrost table after thaw. Furthermore, transcripts involved in acetogenesis were expressed exclusively after thaw suggesting that acetogenic bacteria are a potential source of acetate for acetoclastic methanogenesis in freshly thawed permafrost. Metatranscriptomics is shown here to be a useful approach for inferring the activity of permafrost microbes that has potential to improve our understanding of permafrost SOM bioavailability and biogeochemical mechanisms contributing to greenhouse gas emissions as a result of permafrost thaw.