Nutrient enrichment induces a shift in dissolved organic carbon (DOC) metabolism in oligotrophic freshwater sediments

Authors

F.L. Brailsford, H.C. lanville, P.N. Golyshin, M.R. Marshall, C.E. Lloyd, P.J. Johnes, D.L.Jones

Dissolved organic carbon (DOC) turnover in aquatic environments is modulated by the presence of other key macronutrients, including nitrogen (N) and phosphorus (P). The ratio of these nutrients directly affects the rates of microbial growth and nutrient processing in the natural environment. The aim of this study was to investigate how labile DOC metabolism responds to changes in nutrient stoichiometry using ¹⁴C tracers in conjunction with untargeted analysis of the primary metabolome in upland peat river sediments. N addition led to an increase in ¹⁴C-glucose uptake, indicating that the sediments were likely to be primarily N limited. The mineralisation of glucose to ¹⁴CO₂ reduced following N addition, indicating that nutrient addition induced shifts in internal carbon (C) partitioning and microbial C use efficiency (CUE). This is directly supported by the metabolomic profile data which identified significant differences in 22 known metabolites (34% of the total) and 30 unknown metabolites (16% of the total) upon the addition of either N or P. ¹⁴C-glucose addition increased the production of organic acids known to be involved in mineral P dissolution (e.g. gluconic acid, malic acid). Conversely, when N was not added, the addition of glucose led to the production of the sugar alcohols, mannitol and sorbitol, which are well known microbial C storage compounds. P addition resulted in increased levels of several amino acids (e.g. alanine, glycine) which may reflect greater rates of microbial growth or the P requirement for coenzymes required for amino acid synthesis. We conclude that inorganic nutrient enrichment in addition to labile C inputs has the potential to substantially alter in-stream biogeochemical cycling in oligotrophic freshwaters.

Protistan community composition in anoxic sediments from three salinity-disparate Japanese lakes

Authors

Takafumi Kataoka, Ryuji Kondo

Community composition patterns of benthic protists were investigated in salinity-disparate lakes, including a coastal saline lake (Lake Hiruga), a brackish lake (Lake Suigetsu) and a freshwater lake (Lake Biwa). Samples were collected from the surface layer of anoxic sediment (0–5 cm depth horizon) at each lake; two sets of samples were collected 2 months apart. Sequences of 18S rRNA genes were analysed using high throughput sequencing. We obtained 63,619–389,041 sequences per sample, resulting in 4,331 operational taxonomic units (OTUs) based on 98% similarity. Cluster analysis showed that the community structures between seasons in each lake were similar, while there were marked differences among lakes. Other than photosynthetic organisms, Metazoa and Fungi, 3,018 (70%), 1,132 (26%) and 391 (9%) of protistan OTUs were obtained from lakes Biwa, Hiruga and Suigetsu, respectively. Taxonomic analysis showed 23 OTUs (5.3%) were common to the three lakes, and were composed of 19 Alveolata-, three Stramenopiles- and one unclassified-related taxa. Our results suggest that salinity is an important environmental variable that determines community composition of protists in anoxic sediments in lakes.

Cyanobacterial diversity in the algal–bacterial consortia from Subarctic regions: new insights from the rock baths at White Sea Coast

Authors

A. Kublanovskaya, K. Chekanov, A. Solovchenko, E. Lobakova

Cyanobacteria characterized by exceptional tolerance to environmental stresses often become pioneer settlers in habitats with harsh conditions. There, they can constitute the core of microbial communities. The taxonomic composition of the cyanobacterial component of algal–bacterial consortia dwelling in a habitat with particularly harsh conditions (rock baths at the coast of Kandalaksha Bay of the White Sea) has been elucidated for the first time. Two workflows of the taxonomic analysis of the cyanobacteria were tested including the combinations of two programs and two databases (QIIME+Greengenes and Usearch+NCBI GenBank). Our results obviated the need of the using of a complex approach combining morphological and metagenomic analyses for revealing the taxonomic structure of cyanobacteria in natural habitats. Our results show that the cyanobacterial component of the consortia from the habitats with harsh and highly volatile environmental conditions is enriched with non-diazotrophic and diazotrophic non-branched filamentous cyanobacteria.

Impact of planktonic low nucleic acid-content bacteria to bacterial community structure and associated ecological functions in a shallow lake

Authors

Yuhao Song, Yufeng Wang, Guannan Mao, Guanghai Gao, Yingying Wang

In this study, 0.45 μm filtration, flow cytometric fingerprint, 16S rRNA amplicon sequencing, and bioinformation tools were adopted to analyze the structural diversity and potential functions of planktonic low nucleic acid (LNA)- content bacteria in a shallow lake. Three bacterial groups, namely, “LNA,” “high nucleic acid (HNA)-Small,” and “HNA-Large,” were classified through flow cytometric fingerprint, among which the “HNA-Small” group was possibly in the proliferation stage of the “LNA” group. Total nitrogen and phosphate were the key factors that influence the growth of LNA bacteria. Results of 16S rRNA amplicon sequencing showed that LNA bacteria were phylogenetically less diverse than HNA bacteria, and Actinobacteria and Proteobacteria (especially Gamma-Proteobacteria) were the dominant phyla in LNA bacterial operational taxonomic units (OTUs). Accordingly, hgcI_clade and Pseudomonas were the most abundant bacterial genera in LNA bacterial OTUs. The fraction of low-abundance LNA bacteria was sensitive to several environmental factors, indicating that environmental factors only determined the fraction distribution of low-abundance bacteria. The prediction of metabolic and ecological functions showed that LNA and HNA bacteria had distinct metabolic and ecological functions, which were mainly attributed to the dominant and exclusive bacterial groups.

Elucidating functional microorganisms and metabolic mechanisms in a novel engineered ecosystem integrating C, N, P and S biotransformation by metagenomics

Authors

Yan Zhang, Zheng-shuang Hua, Hui Lu, Adrian Oehmen, Jianhua Guo

Denitrifying sulfur conversion-associated enhanced biological phosphorous removal (DS-EBPR) system is not only a novel wastewater treatment process, but also an ideal model for microbial ecology in a community context. However, it exists the knowledge gap on the roles and interactions of functional microorganisms in the DS-EBPR system for carbon (C), nitrogen (N), phosphorus (P) and sulfur (S) bioconversions. We use genome-resolved metagenomics to build up an ecological model of microbial communities in a lab-scale DS-EBPR system with stable operation for more than 400 days. Our results yield 11 near-complete draft genomes that represent a substantial portion of the microbial community (39.4%). Sulfate-reducing bacteria (SRB) and sulfide-oxidizing bacteria (SOB) promote complex metabolic processes and interactions for C, N, P and S conversions. Bins 1–4 and 10 are considered as new potential polyphosphate-accumulating organisms (PAOs), in which Bins 1–4 can be considered as S-related PAOs (S-PAOs) with no previously cultivated or reported members. Our findings give an insight into a new ecological system with C, N, P and S simultaneous bioconversions and improve the understanding of interactions among SRB, SOB, denitrifiers and PAOs within a community context.

Environmental DNA Time Series in Ecology

Authors

Miklós Bálint, Markus Pfenninger, Hans-Peter Grossart, Pierre Taberlet, Mark Vellend, Mathew A. Leibold, Göran Englund, Diana Bowler

Ecological communities change in time and space, but long-term dynamics at the century-to-millennia scale are poorly documented due to lack of relevant data sets. Nevertheless, understanding long-term dynamics is important for explaining present-day biodiversity patterns and placing conservation goals in a historical context. Here, we use recent examples and new perspectives to highlight how environmental DNA (eDNA) is starting to provide a powerful new source of temporal data for research questions that have so far been overlooked, by helping to resolve the ecological dynamics of populations, communities, and ecosystems over hundreds to thousands of years. We give examples of hypotheses that may be addressed by temporal eDNA biodiversity data, discuss possible research directions, and outline related challenges.

Dynamics and determinants of amoeba community, occurrence and abundance in subtropical reservoirs and rivers

Authors

Kexin Ren, Yuanyuan Xue, Regin Rønnd, Lemian Liu, Huihuang Chen, Christopher Rensing, Jun Yang

Free-living amoebae are widespread in freshwater ecosystems. Although many studies have investigated changes in their communities across space, the temporal variability and the drivers of community changes across different habitat types are poorly understood. A total of 108 surface water samples were collected on a seasonal basis from four reservoirs and two rivers in Xiamen city, subtropical China. We used high throughput sequencing and qPCR methods to explore the occurrence and abundance of free-living amoebae. In total, 335 amoeba OTUs were detected, and only 32 OTUs were shared by reservoir and river habitats. The reservoirs and rivers harbored unique amoebae communities and exhibited distinct seasonal patterns in community composition. High abundance of the 18S rRNA gene of Acanthamoeba was observed in spring and summer, whereas the abundance was low in autumn and winter. In addition, the abundance of Hartmannella was significantly higher when isolated from reservoirs in summer/autumn and from river in spring/summer. Moreover, the temporal patterns of amoebae communities were significantly associated with water temperature, indicating that temperature is an important variable controlling the ecological dynamics of amoebae populations. However, our comparative analysis indicated that both environmental selection, and neutral processes, significantly contributed to amoeba community assembly. The genera detected here include pathogenic species and species that can act as vectors for microbial pathogens, which can cause human infections.

Introduction: Recent developments in cyanobacterial research with special reference to aquatic habitats, molecular ecology and phylogenetic taxonomy

Authors

Eugen Rott, Allan Pentecost, Jan Mareš

The global importance of cyanobacteria is well known from their worldwide distribution and abundance as well as their contribution to atmospheric oxygen. In spite of a long history of cyanobacterial research in microbiology and botany, only a small portion of their high diversity has been recovered and only recently been addressed by molecular and phylogenetic methods. Controversies in traditional and modern approaches to cyanobacterial taxonomy still persist, which has stimulated their discussion within the 20th IAC Symposium. In this special section, we present a set of nine contributions, selecting the most interesting outcomes of the meeting. The molecular approaches applied deal on one hand, with classical single and multilocus phylogenetic taxonomy methods, on the other hand with high-throughput next generation sequencing methods to rapidly identify diversity of cyanobacteria in environmental samples without the possibility to investigate their taxonomic status in depth. The studied ecosystems include a variety of freshwater, brackish and marine, planktonic and benthic habitats from which cyanobacteria were sampled. Study regions comprise temperate, arctic, alpine and tropical environments from four continents. We discuss the salient points of the contributions from this volume and formulate four main issues from which conclusions are drawn in order to contribute to future progress in cyanobacterial research.

Wetland Soil Properties and Resident Bacterial Communities Are Influenced by Changes in Elevation

Authors

Philip O. Lee, Cory Shoemaker, Julie B. Olson

Soils from four sites distributed along an elevation gradient from marsh to coastal forest in a wetland bordering the Gulf of Mexico were sampled over a 16-months period. In addition to measuring a suite of environmental conditions, terminal restriction fragment length polymorphism analyses of the resident bacterial communities were performed. Wetland soil bacterial communities varied across both space and time, with all measured variables (temperature, pH, percentage of soil organic matter, salinity, and concentrations of sulfide, NH₄⁺, NO₃⁻, and soluble reactive phosphorus) showing significant site by time interactions. Analyses of bacterial communities showed both marsh zones (Spartina and Cladium) supported similar communities, as did the ecotone and coastal forest. Bacterial communities within coastal forest soils were significantly different than those within marsh soils, and the ecotone communities were significantly different from the Spartina marsh soil. Temperature and pH were the most influential environmental factors impacting bacterial community composition but no predictable patterns were identified, suggesting that community changes are likely the result of intrinsic factors that are affected by local-scale processes. The dynamic nature of the physiochemical variables within wetlands suggests that more work is needed to determine potential interactive effects on bacterial community structure.

Metagenomic insights into zooplankton‐associated bacterial communities

Authors

Daniele De Corte, Abhishek Srivastava, Marja Koski, Juan Antonio L. Garcia, Yoshihiro Takaki, Taichi Yokokawa, Takuro Nunoura, Nathalie H. Elisabeth, Eva Sintes, Gerhard J. Herndl

Zooplankton and microbes play a key role in the ocean’s biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene, we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton‐associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton‐associated bacterial community is able to colonize the zooplankton’s internal and external surfaces using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton‐associated microbiome suggests that this zooplankton‐associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters.