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The Tibetan Plateau in Northwest China hosts a number of hot springs that represent a biodiversity hotspot for thermophiles, yet their diversity and relationship to environmental conditions are poorly explored in these habitats. In this study we investigated microbial diversity and community composition in 13 Tibetan hot springs with a wide range of temperatures (22.1-75°C) and other geochemical conditions by using the 16S rRNA gene pyrosequencing approach. Bacteria (10(8)-10(11) copy/g; 42 bacterial phyla) in Tibetan hot springs were more abundant and far more diverse than Archaea (10(7)-10(10) copy/g; 5 archaeal phyla). The dominant bacterial phyla systematically varied with temperature. Moderate temperatures (75-66°C) favored Aquificae, GAL35, and novel Bacteria, whereas low temperatures (60-22.1°C) selected for Deinococcus-Thermus, Cyanobacteria, and Chloroflexi. The relative abundance of Aquificae was correlated positively with temperature, but the abundances of Deinococcus-Thermus, Cyanobacteria, and Chloroflexi were negatively correlated with temperature. Cyanobacteria and Chloroflexi were abundant in Tibetan hot springs and their abundances were positively correlated at low temperatures (55-43°C) but negatively correlated at moderate temperatures (75-55°C). These correlation patterns suggest a complex physiological relationship between these two phyla. Most archaeal sequences were related to Crenarchaeota with only a few related to Euryarchaeota and Thaumarchaeota. Despite the fact that microbial composition in Tibetan hot springs was strongly shaped by temperature, microbial diversity (richness, evenness and Shannon diversity) was not significantly correlated with temperature change. The results of this study expand our current understanding of microbial ecology in Tibetan hot springs and provide a basis for a global comparison.

Improper kitchen and agricultural waste management causes substantial health and environmental problems. The microbiological aspects of compost are crucial in optimizing its functionality as an organic fertilizer. This systematic review studies the relationship between kitchen and agricultural waste composts and their bacterial communities as well as the physicochemical properties. A total of 59 publications dated 2010 to 19 June 2023 were included. Results revealed that the pH of these waste composts ranges from 5.0 to 10.0, and the carbon to nitrogen (C/N) ratio values are between 12.70 and 47.00, which are optimal for plant growth. Environmental bacterial phyla such as Acidobacteria, Nitrospirae, Synergistetes, and thermophiles such as Thermodesulfobacteria exclusively exist in agricultural waste compost. These bacteria are pivotal in degrading lignocellulosic biomass and participating in the plant biogeochemical cycles. This study identifies potential strategies in improving the microbiological and abiotic aspects of compost for soil nutrient enrichment in the future, informing the best practice of composting to better manage the waste, and mitigate the environmental pollution, which eventually enhances public health and socioeconomic development of the country.

Eriocheir sinensis is the main aquaculture species in China. With the continuous expansion of the aquaculture scale, the demand for E. sinensis seedlings was also increased. The water used in breeding has well-nourished and its discharge into the sea posed significant risks. This study sampled the wastewater discharge points of the E. sinensis seedlings in Sheyang County, Jiangsu Province, and the areas far from the discharge points that were not affected in March and May 2023, respectively. A large number of antibiotic resistance genes (ARGs) were found in the sediment of the wastewater discharge area, and the highest ARG was sulfonamide ARG- sul1 using qPCR analysis, while ARGs were almost undetectable in the areas not affected by wastewater discharge. The 16S rRNA sequence analysis results showed that the main bacterial phyla at the wastewater discharge point were Bacteroidetes , Proteobacteria , and Thermodesulfobacteria . In the control point, the main bacterial phyla were Proteobacteria , Chlorobacterium , and Thermodesulfobacteria . There were significant differences in the composition of microbial communities between the two points, and the samples at the wastewater discharge point were more clustered and had higher similarity. The correlation network and redundancy analysis indicated that the phyla Bacteroidetes , Firmicutes , and Proteobacteria at the wastewater discharge points were positively correlated with most ARGs. The wastewater discharge had no effect on heavy metals from the two points. This study sets a foundation for future research by identifying key microbial taxa as potential ARG carriers and examining the interactions between microbial communities, ARGs, and heavy metals.

The microbial community structure of sediments in the Bahe River Basin, China was studied using a high-throughput sequencing platform and PCR amplification to investigate the pattern changes in microbial communities in urban rivers affected by anthropogenic activities and their environmental driving mechanisms. The results demonstrated that the average total nitrogen and total phosphorus in the sediments were 524 and 734 mg/kg, respectively. The T, COD and NH4+-N of the water and the moisture content of the sediments has significantly impacted on the microbial community structure. Twenty microbial species with a relative abundance > 1% in the sediments of the river were observed, accounting for 95–99% of the total microbial community. The primary species were Proteobacteria (13.86–69.14%), Firmicutes (1.45–58.33%), Chloroflexi (3.68–26.18%), Actinobacteria (2.7–21.51%), Acidobacteria (0.73–16.36%), Bacteroides (1.53–14.11%), and Thermodesulfobacteria (0.1–8.9%), accounting for over 90% of the total microbial community. At the class level, the primary species were γ-proteobacteria, Alphaproteobacteria, Anaerolineae, Bacillus, Bacteroidota, Actinobacteriota, and Clostridia, accounting for over 70% of the total microbial community. Our results provide direct evidence for a link between microbial community structure and environment factors. This evidence demonstrates that sediment microorganisms can be applied to evaluate urban rivers pollution levels, which can provide a scientific basis for pollution control and management in the urban river affected by human activities.

We investigated the effects of metals and physicochemical variables on the microbes and their metabolisms in the sediments of Guarapiranga reservoir, a tropical eutrophic-hypereutrophic freshwater reservoir located in a highly urbanized and industrialized area in Brazil. The metals cadmium, copper, and chromium showed minor contribution to changes in the structure, composition, and richness of sediment microbial communities and functions. However, the effects of metals on the microbiota are increased when taken together with physicochemical properties, including the sediment carbon and sulfur, the bottom water electrical conductivity, and the depth of the water column. Clearly, diverse anthropic activities, such as sewage discharge, copper sulfate application to control algal growth, water transfer, urbanization, and industrialization, contribute to increase these parameters and the metals spatially in the reservoir. Microbes found especially in metal-contaminated sites encompassed Bathyarchaeia , MBG-D and DHVEG-1, Halosiccatus , Candidatus Methanoperedens, Anaeromyxobacter , Sva0485, Thermodesulfovibrionia , Acidobacteria , and SJA-15, possibly showing metal resistance or acting in metal bioremediation. Knallgas bacteria, nitrate ammonification, sulfate respiration, and methanotrophy were inferred to occur in metal-contaminated sites and may also contribute to metal removal. This knowledge about the sediment microbiota and metabolisms in a freshwater reservoir impacted by anthropic activities allows new insights about their potential for metal bioremediation in these environments. Graphical Abstract

This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (dsrB gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of Proteobacteria and Firmicutes across all the samples. However, Actinobacteria, Thermodesulfobacteria, and Chlorobi were also detected. Phylogenetic analysis indicated that unassigned dsrB sequences were related to Deltaproteobacteria and Nitrospirota superclusters, Euryarchaeota, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of dsrAB-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.

The objectives of this study were to analyze the difference in ways in which metals polluting Brazilian port areas influence bacterial communities and the selection of resistant strains. The hypothesis tested was that port areas would have microbial communities significantly different from a pristine area, mainly due to a greater load of metals found in these areas. Sediment samples were collected in two port areas (Santos and São Sebastião) and one pristine area (Ubatuba). Total DNA was extracted and MiSeq sequencing was performed. A hundred strains were isolated from the same samples and were tested for metal resistance. The community composition was similar in the two port regions, but differed from the pristine area. Microbial diversity was significantly lower in the port areas. The phyla Proteobacteria , Cyanobacteria , and Thermodesulfobacteria exhibited positive correlations with copper and zinc concentrations. Chloroflex , Nitrospirae , Planctomycetes , and Chlorobi exhibited negative correlations with copper, chromium, and zinc. Cr and Zn had higher concentrations at port areas and were responsible to select more metal-resistant strains. Some genera were found to be able to easily develop metal resistance. The most isolated genera were Bacillus , Vibrio , and Pseudomonas . This type of study can illustrate, even in very complex natural environments, the influence of pollution on the community as a whole and the consequences of these changes.

Mercury (Hg) methylation in mangrove sediments can result in the accumulation of neurotoxic methylmercury (MeHg). Identification of Hg methyltransferase gene hgcA provides the means to directly characterize the microbial Hg-methylating consortia in environments. Hitherto, the microbial Hg-methylating community in mangrove sediments was scarcely investigated. An effort to assess the diversity and abundance of hgcA genes and transcripts and link them to Hg and MeHg contents was made in the mangrove intertidal sediments along the urbanized Shenzhen Bay, China. The hgcA genes and transcripts associated with Thermodesulfobacteria [mainly Geobacteraceae, Syntrophorhabdaceae, Desulfobacterales, and Desulfarculales (these four lineages were previously classified into the Deltaproteobacteria taxon)], as well as Euryarchaeota (mainly Methanomicrobia and Theionarchaea) dominated the hgcA-harboring communities, while Chloroflexota, Nitrospirota, Planctomycetota, and Lentisphaerota-like hgcA sequences accounted for a small proportion. The hgcA genes appeared in greater abundance and diversity than their transcript counterparts in each sampling site. Correlation analysis demonstrated that the MeHg content rather than Hg content significantly correlated with the structure of the existent/active hgcA-harboring community and the abundance of hgcA genes/transcripts. These findings provide better insights into the microbial Hg methylation drivers in mangrove sediments, which could be helpful for understanding the MeHg biotransformation therein.

Trans–Himalayan hot spring waters rich in sulfur, boron, sodium and chlorine (but poor in calcium and silicon) are known based on PCR–amplified 16S rRNA gene sequence data to harbor high diversities of infiltrating bacterial mesophiles. Yet, little is known about the population dynamics, primary productivity, mutual interactions, and thermal adaptations of the microorganisms present in the steaming waters discharged by these geochemically peculiar spring systems. We revealed these aspects of a bacteria–dominated microbiome thriving in the boiling (85°C) fluid vented by a sulfur–borax spring called Lotus Pond, situated at 4436 m above the mean sea–level, in the Puga valley of eastern Ladakh, on the Changthang plateau. Assembly, annotation, and population–binning of >15–GB metagenomic sequence illuminated the numeral predominance of Aquificae (particularly, the genera Hydrogenobacter and Sulfurihydrogenibium), even as Proteobacteria, and Firmicutes, Cyanobacteria, Chloroflexi and Bacteroidetes, contributed most of the genetic diversity of the microbiome; prevalence and diversity of Deinococcus–Thermus, Thermotogae, Thermodesulfobacteria, Crenarchaeota and Euryarchaeota were far less. Perpetual presence of bacterial mesophiles in Lotus Pond vent–water was evident from the detection of 51 such genera that had been discovered in previous 16S–amplicon–based investigations of the habitat, but have no member with laboratory growth at >45°C. The metagenome was replete with genes crucial for hydrothermal, and other stress, adaptations, and a majority of them were attributed to phylogenetic relatives of mesophilic bacteria; examples included genes encoding heat shock proteins, molecular chaperones, and chaperonin complexes; proteins controlling/modulating/inhibiting DNA gyrase; universal stress proteins; methionine sulfoxide reductases; fatty acid desaturases; different toxin–antitoxin systems; enzymes protecting against oxidative damage; proteins conferring flagellar structure/function, chemotaxis, cell adhesion/aggregation, biofilm formation, and quorum sensing. The Lotus Pond Aquificae not only dominated the microbiome numerically but also acted potentially as the main primary producers of the ecosystem, with chemolithotrophic sulfur oxidation (Sox) being the fundamental bioenergetic mechanism, and reductive tricarboxylic acid (rTCA) cycle the predominant carbon fixation pathway. Furthermore, the Aquificae members present in situ contained copious genes for virulence functions, and biosynthesis of the antibiotics monobactams, streptomycin, prodigiosin, acarbose and validamycin, novobiocin, carbapenems, and vancomycin (a few genes were there for phenazine, and neomycin/kanamycin/gentamicin as well). The Lotus Pond Aquificae also contained copious genes for resistance against beta–lactam antibiotics (penicillins, cephalosporins, monobactams, and carbapenems) cationic antimicrobial peptides, vancomycin, aminoglycosides (streptomycin and neomycin/kanamycin/gentamicin), and fluoroquinolones; they also had several genes for multidrug resistance efflux pumps. Among the other thermophiles present, only Thermodesulfobacteria and Deinococcus–Thermus had genes for all these functions, albeit at much lesser frequencies; the Archaea and Thermotogae were either devoid of, or had very few genes for, the aforesaid functions. The Lotus Pond mesophiles, led by Alphaproteobacteria and Gammaproteobacteria, possessed a slightly wider variety, and higher abundance, of antibiotic synthesis/resistance genes, compared with the Aquificae, besides having a more uniform gene count across the antibiotics synthesized/resisted. We hypothesize that antibiosis helped Aquificae avoid niche overlap with other thermophiles/hyperthermophiles, especially the Archaea, besides exacerbating the bioenergetic costs of thermal endurance for the mesophiles infiltrating the system, thereby keeping the potential proliferation of these intruders at bay.Competing Interest StatementThe authors have declared no competing interest.Footnotes* This revised version of the manuscript has been meticulously restructured and modified, incorporating new findings and illustrations.

Nitrospirae spp. distantly related to thermophilic, sulfate-reducing Thermodesulfovibrio species are regularly observed in environmental surveys of anoxic marine and freshwater habitats. However, little is known about their genetic make-up and physiology. Here, we present the draft genome of Nitrospirae bacterium Nbg-4 as a representative of this clade and analyzed its in situ protein expression under sulfate-enriched and sulfate-depleted conditions in rice paddy soil. The genome of Nbg-4 was assembled from replicated metagenomes of rice paddy soil that was used to grow rice plants in the presence and absence of gypsum (CaSO4x2H2O). Nbg-4 encoded the full pathway of dissimilatory sulfate reduction and showed expression thereof in gypsum-amended anoxic bulk soil as revealed by parallel metaproteomics. In addition, Nbg-4 encoded the full pathway of dissimilatory nitrate reduction to ammonia, which was expressed in bulk soil without gypsum amendment. The relative abundance of Nbg-4-related metagenome reads was similar under both treatments indicating that it maintained stable populations while shifting its energy metabolism. Further genome reconstruction revealed the potential to utilize butyrate, formate, H2, or acetate as electron donor, with the Wood-Ljungdahl pathway being expressed under both conditions. Comparison to publicly available Nitrospirae genome bins confirmed that the pathway for dissimilatory sulfate reduction is also present in related Nitrospirae recovered from groundwater. Subsequent phylogenomics showed that such microorganisms form a novel genus within the phylum Nitrospirae, with Nbg-4 as a representative species. Based on the widespread occurrence of this novel genus, we propose for Nbg 4 the name Candidatus Sulfobium mesophilum, gen. nov., spec. nov.