Hypersaline sapropels act as hotspots for microbial dark matter

Niche Differentiation of Biofilm Microorganisms in a Full-scale Municipal Drinking Water Distribution System in China and Their Implication for Biofilm Control

Biofilms on the inner surface of a drinking water distribution system (DWDS) affect water quality and stability. Understanding the niche differentiation of biofilm microbial communities is necessary for the efficient control of DWDS biofilms. However, biofilm studies are difficult to conduct in the actual DWDS because of inaccessibility to the pipes buried underground. Taking the opportunity of infrastructure construction and relevant pipeline replacement in China, biofilms in a DWDS (a water main and its branch pipes) were collected in situ, followed by analysis on the abundances and community structures of bacterial and archaeal using quantitative PCR and high-throughput sequencing, respectively. Results showed that archaea were detected only in the biofilms of the water main, with a range of 9.4×103~1.1×105 copies/cm2. By contrast, bacteria were detected in the biofilms of branch pipes and the distal part of the water main, with a range of 8.8×103~9.6×106 copies/cm2. Among the biofilm samples, the archaeal community in the central part of the water main showed the highest richness and diversity. Nitrosopumilus was found to be predominant (86.22%) in the biofilms of the proximal part of the water main. However, Methanobrevibacter (87.15%) predominated in the distal part of the water main. The bacterial community of the water main and branch pipes was primarily composed of Firmicutes and Proteobacteria at the phylum level, respectively. Regardless of archaea or bacteria, only few operational taxonomic units (OTUs) (<0.5% of total OTUs) were shared by all the biofilms, indicating the niche differentiation of biofilm microorganisms. Moreover, the high Mn content in the biofilms of the distal sampling location (D3) in the water main was linked to the predominance of Bacillus. Functional gene prediction revealed that the proportion of infectious disease-related genes was 0.44-0.67% in the tested biofilms. Furthermore, functional genes related to the resistance of the bacterial community to disinfections and antibiotics were detected in all the samples, that is, glutathione metabolism-relating genes (0.14-0.65%) and beta-lactam resistance gene (0.01-0.05%). The results of this study indicate the ubiquity of archaea and bacteria in the biofilms of water main and branch pipes, respectively, and pipe diameters could be a major influencing factor on bacterial community structure. In the water main, the key finding was the predominant existence of archaea, particularly Nitrosopumilus and methanogen. Hence, their routine monitoring and probable influences on water quality in pipelines with large diameter should be given more attention. Besides, since Mn-related Bacillus and suspected pathogenic Enterococcus were detected in the biofilm, supplementation of disinfectant may be a feasible strategy for inhibiting their growth and ensuring water quality. In addition, the monitoring on their abundance variation could help to determine the frequency and methods of pipeline maintenance.

Haloalkalitolerant Fungi from Sediments of the Big Tambukan Saline Lake (Northern Caucasus): Diversity and Antimicrobial Potential

We have performed a characterization of cultivated haloalkalitolerant fungi from the sediments of Big Tambukan Lake in order to assess their biodiversity and antimicrobial activity. This saline, slightly alkaline lake is known as a source of therapeutic sulfide mud used in sanatoria of the Caucasian Mineral Waters, Russia. Though data on bacteria and algae observed in this lake are available in the literature, data on fungi adapted to the conditions of the lake are lacking. The diversity of haloalkalitolerant fungi was low and represented by ascomycetes of the genera Acremonium, Alternaria, Aspergillus, Chordomyces, Emericellopsis, Fusarium, Gibellulopsis, Myriodontium, Penicillium, and Pseudeurotium. Most of the fungi were characterized by moderate alkaline resistance, and they tolerated NaCl concentrations up to 10% w/v. The analysis of the antimicrobial activity of fungi showed that 87.5% of all strains were active against Bacillus subtilis, and 39.6% were also determined to be effective against Escherichia coli. The majority of the strains were also active against Aspergillus niger and Candida albicans, about 66.7% and 62.5%, respectively. These studies indicate, for the first time, the presence of polyextremotolerant fungi in the sediments of Big Tambukan Lake, which probably reflects their involvement in the formation of therapeutic muds.

Composition of Particulate Matter and Bacterial Community in Gut Contents and Surrounding Sediments of Three Sipunculan Species (Siphonosoma australe, Phascolosoma arcuatum, and Sipunculus nudus)

Siphonosoma australe, Phascolosoma arcuatum, and Sipunculus nudus are three important sipunculan species in tropical intertidal zones. In this study, the particle size, organic matter content, and bacterial community composition in the gut contents of three different sipunculans and their surrounding sediments were analyzed. The grain size fractions of sipunculans' guts were significantly different from those of their surrounding sediments; particle size fractions < 500 μm were favored by the sipunculans. As for the total organic matter (TOM), higher contents of organic matter were observed in the guts than in the surrounding sediments in all three sipunculan species. The bacterial community composition of all the samples was investigated by 16S rRNA gene sequencing, in which a total of 8974 OTUs were obtained from 24 samples based on a 97% threshold. The predominant phylum identified from the gut contents of three sipunculans was Planctomycetota, while the predominant phylum in their surrounding sediments was Proteobacteria. At the genus level, the most abundant genus was Sulfurovum (average 4.36%) in the surrounding sediments, while the most abundant genus was Gplla (average 12.76%) in the gut contents. The UPGMA tree showed that the samples from the guts of three different sipunculans and their surrounding sediments were clustered separately into two groups, which showed that these three sipunculans had a different bacterial community composition with their surrounding sediments. The grain size and total organic matter (TOM) had the greatest impacts on the bacterial community composition at both the phylum and genus levels. In conclusion, the differences in particle size fractions, organic matter content, and bacterial community composition between the gut contents and surrounding sediments in these three sipunculan species might be caused by their selective ingestion.

Asgard archaea in saline environments

Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.

Comprehensive mineralogical and physicochemical characterization of recent sapropels from Romanian saline lakes for potential use in pelotherapy

In this study we aimed to compare the mineralogical, thermal, physicochemical, and biological characteristics of recent organic carbon-rich sediments (‘sapropels’) from three geographically distant Romanian lakes (Tekirghiol and Amara, SE Romania, and Ursu, Central Romania) with distinct hydrogeochemical origins, presently used for pelotherapy. The investigated lakes were classified as inland brackish Na-Cl-sulfated type (Amara), coastal moderately saline and inland hypersaline Na-Cl types (Tekirghiol and Ursu, respectively). The settled organic matter is largely composed of photosynthetic pigments derived from autochthonous phytoplankton. Kerogen was identified in the sapropel of coastal Tekirghiol Lake suggesting its incipient maturation stage. The mineral composition was fairly similar in all sapropels and mainly consisted of quartz, calcite, and aragonite. Smectite, illite, mixed layer smectite/illite appeared as major clay components. Potentially toxic elements were found in low concentrations. The physical properties (i.e., specific heat, thermal conductivity and retentivity) and cation exchange capacity are comparable to other peloids used for therapy. This study is the first comprehensive multi-approached investigation of the geochemical nature of recent sapropels in Romanian saline lakes and thus contributes to expanding our knowledge on the origin and physicochemical qualities of organic matter-rich peloids with therapeutic uses.

A network approach to elucidate and prioritize microbial dark matter in microbial communities

Microbes compose most of the biomass on the planet, yet the majority of taxa remain uncharacterized. These unknown microbes, often referred to as “microbial dark matter,” represent a major challenge for biology. To understand the ecological contributions of these Unknown taxa, it is essential to first understand the relationship between unknown species, neighboring microbes, and their respective environment. Here, we establish a method to study the ecological significance of “microbial dark matter” by building microbial co-occurrence networks from publicly available 16S rRNA gene sequencing data of four extreme aquatic habitats. For each environment, we constructed networks including and excluding unknown organisms at multiple taxonomic levels and used network centrality measures to quantitatively compare networks. When the Unknown taxa were excluded from the networks, a significant reduction in degree and betweenness was observed for all environments. Strikingly, Unknown taxa occurred as top hubs in all environments, suggesting that “microbial dark matter” play necessary ecological roles within their respective communities. In addition, novel adaptation-related genes were detected after using 16S rRNA gene sequences from top-scoring hub taxa as probes to blast metagenome databases. This work demonstrates the broad applicability of network metrics to identify and prioritize key Unknown taxa and improve understanding of ecosystem structure across diverse habitats.

A Systematic Study of the Limits of Life in Mixed Ion Solutions: Physicochemical Parameters Do Not Predict Habitability

This study investigated what defines the limits of life in mixed ion solutions. Better understanding these limits should allow us to better predict the habitability of extreme environments on the Earth and extraterrestrial environments. We systematically examined the response of Bacillus subtilis, a well characterized non-halophile model organism, to a range of solutions made from single and mixed salts up to their solubility limits and measured at what concentration growth was arrested, specifically exploring Na, Mg, and Ca cations and Cl, SO4, and ClO4 anions. We measured the physicochemical properties of the solutions to identify which properties correlated with the limits of growth. Individual salts imposed a growth limit specific to the combination of cation and anion, although we generally observe that chloride salts allow growth at lower water activity than sulfate salts, with perchlorate restricting growth even at the highest measured water activity. Growth was limited at a wide range of ionic strength, with no apparently correlation. Despite the theoretically counteracting disordering effects (chaotropic) of perchlorates and ordering effects (kosmotropic) effects of sulfates, when these salts were combined they instead additively narrowed the window for growth in both the Na and Mg cation systems, in the same manner as the combined effects of two chaotropic Ca salts. Our results imply that away from hard limits that might be imposed by physicochemical properties such as water activity, ionic strength or chaotropicity in highly concentrated brines, these properties do not set the limits of life. Instead these limits are highly specific to the salts and organisms in question. This specificity means that the habitability of extreme environments cannot be predicted, even with accurate measurements of the physicochemical conditions present.

Ecology and physiology of halophilic microorganisms - Thematic issue based on papers presented at Halophiles 2019 - 12th International Conference on Halophilic Microorganisms, Cluj-Napoca, Romania, 24-28 June, 2019

In June 2019, the 12th International Conference on Halophilic Microorganisms - Halophiles 2019, was held in Cluj-Napoca, Romania. This thematic issue of FEMS Microbiology Letters contains papers based on lectures and posters presented at the conference. We here provide a short overview of past research on hypersaline environments in Romania and the microorganisms inhabiting them, and briefly present the papers published in this thematic issue.

Spatio-temporal insights into microbiology of the freshwater-to-hypersaline, oxic-hypoxic-euxinic waters of Ursu Lake

Ursu Lake is located in the Middle Miocene salt deposit of Central Romania. It is stratified, and the water column has three distinct water masses: an upper freshwater-to-moderately saline stratum (0-3 m), an intermediate stratum exhibiting a steep halocline (3-3.5 m), and a lower hypersaline stratum (4 m and below) that is euxinic (i.e. anoxic and sulphidic). Recent studies have characterized the lake's microbial taxonomy and given rise to intriguing ecological questions. Here, we explore whether the communities are dynamic or stable in relation to taxonomic composition, geochemistry, biophysics, and ecophysiological functions during the annual cycle. We found: (i) seasonally fluctuating, light-dependent communities in the upper layer (≥0.987-0.990 water-activity), a stable but phylogenetically diverse population of heterotrophs in the hypersaline stratum (water activities down to 0.762) and a persistent plate of green sulphur bacteria that connects these two (0.958-0.956 water activity) at 3-3.5 to 4 m; (ii) communities that might be involved in carbon- and sulphur-cycling between and within the lake's three main water masses; (iii) uncultured lineages including Acetothermia (OP1), Cloacimonetes (WWE1), Marinimicrobia (SAR406), Omnitrophicaeota (OP3), Parcubacteria (OD1) and other Candidate Phyla Radiation bacteria, and SR1 in the hypersaline stratum (likely involved in the anaerobic steps of carbon- and sulphur-cycling); and (iv) that species richness and habitat stability are associated with high redox-potentials. Ursu Lake has a unique and complex ecology, at the same time exhibiting dynamic fluctuations and stability, and can be used as a modern analogue for ancient euxinic water bodies and comparator system for other stratified hypersaline systems.

Bioturbation of peanut worms Sipunculus nudus on the composition of prokaryotic communities in a tidal flat as revealed by 16S rRNA gene sequences

To understand the impacts of peanut worms Sipunculus nudus on the prokaryotic community composition in a tidal flat, an onsite investigation was conducted in Suixi in the Beibu Gulf (109.82E, 21.35N) in the burrow sediments, non‐burrow sediments and the sediments without peanut worm disturbance (control). The16S rRNA gene Illumina MiSeq sequencing was used to investigate the microbial communities and their response to bioturbation by S. nudus in a sandy tidal flat. A total of 18 bacteria phyla were detected, and Proteobacteria and Cyanobacteria constituted the majority of the prokaryotic community in the samples. The distribution of the relative abundances of genera showed that approximately 6.99%–17% of the reads in the samples were classified into 25 known genera. Sulfate‐reducing bacteria (Desulfococcus and Desulfosarcina) were the most abundant taxa, followed by Thermodesulfovibrionaceae LCP‐6, indicating that sulfate reduction is the main process in the sandy tidal flat. The abundances of Desulfococcus, LCP‐6 and Cyanobacterium in the non‐burrow sediment were greater than in the burrow sediment, suggesting that the anoxic condition is more suitable for Desulfococcus and LCP‐6 when the activity of S. nudus is absent. The biomass of Cyanobacterium was decreased by the feeding bioturbation of S. nudus. Meanwhile, the relative abundance of the Bacteroidetes Luteimonas in the burrow sediments was significantly greater than in the non‐burrow sediment, and there was a strong relationship between S. nudus bioturbation and increased in oxygen contents and oxidation‐reduction potentials in the burrow sediment. The abundances of Desulfococcus and LCP‐6 were greater in the middle layer (20–30 cm) than in the top layer in the non‐burrow sediment. However, the middle and bottom layers (20–30, 30–40 cm) had higher abundances of these genera than did the upper layers (0–10, 10–20 cm) in the burrow sediments. The abundances of the Fusobacteria Propionigenium and the Spirochaetes Spirochaeta were greater in the middle and bottom layers (20–30 cm, 30–40 cm) than in the top layers (0–10, 10–20 cm) in the burrow sediment, but this phenomenon was not found in the non‐burrow sediment. This study demonstrates that bioturbation by S. nudus plays an important role in reshaping the bacterial community composition in intertidal regions.