Metagenomic analysis further extends the role of Chloroflexi in fundamental biogeochemical cycles

Discovery and biocatalytic characterization of opine dehydrogenases by metagenome mining

Enzymatic processes play an increasing role in synthetic organic chemistry which requires the access to a broad and diverse set of enzymes. Metagenome mining is a valuable and efficient way to discover novel enzymes with unique properties for biotechnological applications. Here, we report the discovery and biocatalytic characterization of six novel metagenomic opine dehydrogenases from a hot spring environment (mODHs) (EC 1.5.1.X). These enzymes catalyze the asymmetric reductive amination between an amino acid and a keto acid resulting in opines which have defined biochemical roles and represent promising building blocks for pharmaceutical applications. The newly identified enzymes exhibit unique substrate specificity and higher thermostability compared to known examples. The feature that they preferably utilize negatively charged polar amino acids is so far unprecedented for opine dehydrogenases. We have identified two spatially correlated positions in their active sites that govern this substrate specificity and demonstrated a switch of substrate preference by site-directed mutagenesis. While they still suffer from a relatively narrow substrate scope, their enhanced thermostability and the orthogonality of their substrate preference make them a valuable addition to the toolbox of enzymes for reductive aminations. Importantly, enzymatic reductive aminations with highly polar amines are very rare in the literature. Thus, the preparative-scale enzymatic production, purification, and characterization of three highly functionalized chiral secondary amines lend a special significance to our work in filling this gap. KEY POINTS: • Six new opine dehydrogenases have been discovered from a hot spring metagenome • The newly identified enzymes display a unique substrate scope • Substrate specificity is governed by two correlated active-site residues.

The response of C/N/S cycling functional microbial communities to redox conditions in shallow aquifers using in-situ sediment as bio-trap matrix

Microbial communities are fundamental components driving critical biogeochemical carbon (C), nitrogen (N) and sulfur (S) cycles in groundwater ecosystems. The reduction-oxidation (redox) potential is one important environmental factor influencing the microbial community composition. Here, we developed a bio-trap method using in-situ sediment as a matrix to collect aquifer sediment samples and evaluate the response of microbial composition and C/N/S cycling functions to redox variations created by providing sole O2, joint O2 and H2, and sole H2 to three wells. Illumina sequencing analyses showed that the microbial communities in the bio-trap sediment could respond quickly to redox changes in the wells, demonstrating that this bio-trap method is promising for detecting microbial variation in the aquifer sediment. The microbial metabolic functions related to C, N and S cyclings and organic pollutants degradation were predicted by the Kyoto Encyclopedia of Genes and Genomes (KEGG) approach. It was found that the joint O2 and H2 injection produced medium oxidation-reduction potential (ORP -346 and -614 mV) and enhanced more microbial functions than sole O2 or H2, which mainly include oxidative phosphorylation, most carbon source metabolism, various pollutants degradation, and nitrogen and sulfur metabolism. Moreover, the functional genes encoding phenol monooxygenase, dioxygenase, nitrogen fixation, nitrification, aerobic and anaerobic nitrate reductase, nitrite reductase, nitric oxide reductase, and sulfur oxidation increased. These findings tell us the contaminant bioremediation and N, S metabolism can be promoted by adjusting ORP realised by injecting joint O2 and H2.

Phages enhance both phytopathogen density control and rhizosphere microbiome suppressiveness

Bacteriophages, viruses that specifically target plant pathogenic bacteria, have emerged as a promising alternative to traditional agrochemicals. However, it remains unclear how phages should be applied to achieve efficient pathogen biocontrol and to what extent their efficacy is shaped by indirect interactions with the resident microbiota. Here, we tested if the phage biocontrol efficacy of Ralstonia solanacearum phytopathogenic bacterium can be improved by increasing the phage cocktail application frequency and if the phage efficacy is affected by pathogen-suppressing bacteria already present in the rhizosphere. We find that increasing phage application frequency improves R. solanacearum density control, leading to a clear reduction in bacterial wilt disease in both greenhouse and field experiments with tomato. The high phage application frequency also increased the diversity of resident rhizosphere microbiota and enriched several bacterial taxa that were associated with the reduction in pathogen densities. Interestingly, these taxa often belonged to Actinobacteria known for antibiotics production and soil suppressiveness. To test if they could have had secondary effects on R. solanacearum biocontrol, we isolated Actinobacteria from Nocardia and Streptomyces genera and tested their suppressiveness to the pathogen in vitro and in planta. We found that these taxa could clearly inhibit R. solanacearum growth and constrain bacterial wilt disease, especially when combined with the phage cocktail. Together, our findings unravel an undiscovered benefit of phage therapy, where phages trigger a second line of defense by the pathogen-suppressing bacteria that already exist in resident microbial communities.

IMPORTANCE

Ralstonia solanacearum is a highly destructive plant-pathogenic bacterium with the ability to cause bacterial wilt in several crucial crop plants. Given the limitations of conventional chemical control methods, the use of bacterial viruses (phages) has been explored as an alternative biological control strategy. In this study, we show that increasing the phage application frequency can improve the density control of R. solanacearum, leading to a significant reduction in bacterial wilt disease. Furthermore, we found that repeated phage application increased the diversity of rhizosphere microbiota and specifically enriched Actinobacterial taxa that showed synergistic pathogen suppression when combined with phages due to resource and interference competition. Together, our study unravels an undiscovered benefit of phages, where phages trigger a second line of defense by the pathogen-suppressing bacteria present in resident microbial communities. Phage therapies could, hence, potentially be tailored according to host microbiota composition to unlock the pre-existing benefits provided by resident microbiota.

Biosynthetic potential of uncultured anammox community bacteria revealed through multi-omics analysis

Microbial secondary metabolites (SMs) and their derivatives have been widely used in medicine, agriculture, and energy. Growing needs for renewable energy and the challenges posed by antibiotic resistance, cancer, and pesticides emphasize the crucial hunt for new SMs. Anaerobic ammonium-oxidation (anammox) systems harbor many uncultured or underexplored bacteria, representing potential resources for discovering novel SMs. Leveraging HiFi long-read metagenomic sequencing, 1,040 biosynthetic gene clusters (BGCs) were unearthed from the anammox microbiome with 58% being complete and showcasing rich diversity. Most of them showed distant relations to known BGCs, implying novelty. Members of the underexplored lineages (Chloroflexota and Planctomycetota) and Proteobacteria contained lots of BGCs, showcasing substantial biosynthetic potential. Metaproteomic results indicated that Planctomycetota members harbored the most active BGCs, particularly those involved in producing potential biofuel-ladderane. Overall, these findings underscore that anammox microbiomes could serve as valuable resources for mining novel BGCs and discovering new SMs for practical application.

Impact of bioelectricity on DNRA process and microbial community composition within cathodic biofilms in dual-chambered bioelectrode microbial fuel cell (MFC)

The synchronous bioelectricity generation and dissimilatory nitrate reduction to ammonium (DNRA) pathway in Klebsiella variicola C1 was investigated. The presence of bioelectricity facilitated cell growth on the anodic biofilms, consequently enhancing the nitrate removal efficiency decreasing total nitrogen levels and causing a negligible accumulation of NO2- in the supernatant. Genomic analysis revealed that K. variicola C1 possessed a complete DNRA pathway and largely annotated electron shuttles. The up-regulated expression of genes narG and nirB, encoding nitrite oxidoreductase and nitrite reductase respectively, was closely associated with increased extracellular electron transfer (EET). High-throughput sequencing analysis was employed to investigate the impact of bioelectricity on microbial community composition within cathodic biofilms. Results indicated that Halomonas, Marinobacter and Prolixibacteraceae were enriched at the cathode electrodes. In conclusion, the integration of a DNRA strain with MFC facilitated the efficient removal of wastewater containing high concentrations of NO3- and enabled the environmentally friendly recovery of NH4+.

The relationship between gastric microbiome features and responses to neoadjuvant chemotherapy in gastric cancer

Background

Emerging evidence demonstrates that the gastrointestinal microbiome has the potential to be a biomarker in neoadjuvant chemoradiotherapy for colorectal cancer (CRC). Yet studies on the impact of the gastric microbiome (GM) on the response to neoadjuvant chemotherapy (NACT) are still scarce.

Methods

Forty-eight patients with gastric cancer participated in this retrospective study, and 16S rRNA sequencing was performed to evaluate formalin-fixed and paraffin-embedded (FFPE) tissue biospecimens and fresh-frozen tissues.

Results

In this study, 16 bacterial taxa at different levels, including Bacillus, Anaerococcus, and Chloroflexi, were identified to be enriched before NACT in response (R) patients in group FFPE. In contrast, 6 bacterial taxa, such as Haemophilus, Veillonellaceae (Veillonella), etc. were enriched after NACT, in which we reported for the first time that the phylum Chloroflexi was enriched before NACT in R patients. Thirty-one bacterial taxa of Coriobacteriaceae, Ruminococcaceae, Veillonellaceae, and Lachnospiraceae were identified in group mucosa as being enriched in R patients. In comparison, 4 bacterial taxa dominated by the phylum Proteobacteria were enriched in NR patients. Notably, the family Veillonellaceae was found in both tissue samples, and the metabolic pathways, including the citrate cycle (TCA cycle) and various amino acids, including alanine, were found to be potentially predictive in both sample species.

Conclusion

There are differences in the features of the GM for different NACT response results. The causal relationship deserves to be confirmed by further investigations.

Genome-based approach to evaluate the metabolic potentials and exopolysaccharides production of Bacillus paralicheniformis CamBx3 isolated from a Chilean hot spring

In the present study, a thermophilic strain designated CamBx3 was isolated from the Campanario hot spring, Chile. Based on 16S rRNA gene sequence, phylogenomic, and average nucleotide identity analysis the strain CamBx3 was identified as Bacillus paralicheniformis. Genome analysis of B. paralicheniformis CamBx3 revealed the presence of genes related to heat tolerance, exopolysaccharides (EPS), dissimilatory nitrate reduction, and assimilatory sulfate reduction. The pangenome analysis of strain CamBx3 with eight Bacillus spp. resulted in 26,562 gene clusters, 7,002 shell genes, and 19,484 cloud genes. The EPS produced by B. paralicheniformis CamBx3 was extracted, partially purified, and evaluated for its functional activities. B. paralicheniformis CamBx3 EPS with concentration 5 mg mL-1 showed an optimum 92 mM ferrous equivalent FRAP activity, while the same concentration showed a maximum 91% of Fe2+ chelating activity. B. paralicheniformis CamBx3 EPS (0.2 mg mL-1) demonstrated β-glucosidase inhibition. The EPS formed a viscoelastic gel at 45°C with a maximum instantaneous viscosity of 315 Pa.s at acidic pH 5. The present study suggests that B. paralicheniformis CamBx3 could be a valuable resource for biopolymers and bioactive molecules for industrial applications.

Seasonal and distance-decay patterns of surface sediments microbial nitrogen and sulfur cycling linkage in the eastern coast of China

The surface sediments as a repository of pelagic environment changes and microbial community structural succession tend to have a profound effect on global and local nitrogen and sulfur cycling. In this study, analysis of sediment samples collected from the Bohai Sea, Yellow Sea, and north of the East China Seas (BYnECS) revealed longitude, latitude, depth, and chlorophyll had the strongest influence on microbial community structure (p-values < 0.005). A clear distance-decay pattern was exhibited in BYnECS. The result of co-occurrence network modularization implied that the more active pathway in winter was thiosulfate reduction and nitrate reduction, while in summer it was nitrification. The potential functional genes were predicted in microbial communities, and the most dominant genes were assigned to assimilatory sulfur reduction, denitrification, and dissimilatory nitrate reduction. This study innovatively explored the potential relationships between nitrogen and sulfur cycling genes of these three sea regions in the China Sea.

Phylogenomic discernments into Anaerolineaceae thermal adaptations and the proposal of a candidate genus Mesolinea

This study delves into the evolutionary history of Anaerolineaceae, a diverse bacterial family within the Chloroflexota phylum. Employing a multi-faceted approach, including phylogenetic analyses, genomic comparisons, and exploration of adaptive features, the research unveils novel insights into the family's taxonomy and evolutionary dynamics. The investigation employs metagenome-assembled genomes (MAGs), emphasizing their prevalence in anaerobic environments. Notably, a novel mesophilic lineage, tentatively named Mesolinea, emerges within Anaerolineaceae, showcasing a distinctive genomic profile and apparent adaptation to a mesophilic lifestyle. The comprehensive genomic analyses shed light on the family's complex evolutionary patterns, including the conservation of key operons in thermophiles, providing a foundation for understanding the diverse ecological roles and adaptive strategies of Anaerolineaceae members.

Peracetic acid pretreatment improves biogas production from anaerobic digestion of sewage sludge by promoting organic matter release, conversion and affecting microbial community

Peracetic acid (PAA) pretreatment is considered as a novel and effective chemical pretreatment method for sludge. However, there is little information available on potential mechanisms of how PAA pretreatment affects sludge anaerobic digestion (AD). To fill the knowledge gap, this study investigated the effects and potential mechanisms of PAA pretreatment on sludge AD systems from physicochemical and microbiological perspectives. Batch experiments resulted that biogas production was enhanced by PAA pretreatment and the highest cumulative biogas yield (297.94 mL/g VS (volatile solid)) was obtained with 2 mM/g VS of PAA pretreatment. Kinetic model analysis illustrated that the PAA pretreatment improved the biogas potential (Pt) of sludge AD, but prolonged the lag phase (λ) of AD. Mechanistic studies revealed that reactive oxygen species (ROS) (HO•, O2-•, 1O2 and CH3C(O)OO•) were the major intermediate products of PAA decomposition. These ROS effectively promoted the decomposition and solubilization of sludge, and provided more biodegradable organic matter for the following AD reactions. 16S rRNA amplicon sequencing showed that some functional microorganisms associated with hydrolysis, acidogenesis, acetogenesis as well as methanogenesis, such as Hydrogenispora, Romboutsia, Longivirga, Methanosarcina and Methanosaet, were significantly enriched in reactors pretreated with PAA. Redundancy analysis and variation partitioning analysis indicated that functional microorganisms were significantly correlated with intermediate metabolites (soluble carbohydrate, soluble protein, soluble chemical oxygen demand and volatile fatty acids) and cumulative biogas production. This study provides a fresh understanding of the effects and mechanisms of PAA pretreatment on sludge AD, updates the insights into the response of functional microorganisms to PAA pretreatment, and the findings obtained might provide a fundamental basis for chemical pretreatment of sludge AD using oxidants.

Algae-Bacteria cooperated microbial ecosystem: A self-circulating semiartificial photosynthetic purifying strategy

The microbial fuel cell (MFC) is a promising bio-electrochemical technology that enables simultaneous electricity generation and effluent purification. Harnessing solar energy to provide sustainable power for MFC operation holds great potential. In this study, a semiartificial photosynthetic self-circulating MFC ecosystem is successfully established through the collaboration of electrogenic microorganisms and photosynthetic algae. The ecosystem can operate continuously without carbon sources and produces a voltage of 150 mV under irradiation. The irradiation doubles the maximum power density of the ecosystem, reaching 8.07 W/m2 compared to dark conditions. The results of cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) suggest a higher diffusion capacity or faster electron replenishment ability within the ecosystem. Furthermore, the capacity of ecosystem for removing chromium (Cr(VI)) has been investigated comprehensively. Under irradiation, the ecosystem demonstrates a 2.25-fold increase in Cr(VI) removal rate compared to dark conditions. Finally, the results of 16S rRNA amplicon sequencing indicates an increase in the relative abundance of strict and facultative aerobic electroactive bacteria in the ecosystem, including Citrobacter (21 %), Bacillus (15 %) and Enterococcus (6 %). The ecosystem offers a novel, self-sustaining approach to address the challenges of energy recovery and environmental pollution.

Impacts of Thermal Drainage on Bacterial Diversity and Community Construction in Tianwan Nuclear Power Plant

As one of the low-carbon and high-efficient energy sources, nuclear power is developing vigorously to alleviate the crisis of global climate warming and realize carbon neutrality goals. Meanwhile, the ecological effect of thermal drainage in the nuclear power plant is significantly remarkable, which environmental assessment system has not yet referred to microorganisms. The rapid response of microbial diversity and community structure to environmental changes is crucial for ecosystem stability. This study investigated the bacterial diversity, community construction, and the co-occurrence patterns by 16S rRNA gene amplicon sequencing among gradient warming regions in Tianwan Nuclear Power Plant. The alpha diversity of the high warming region was the lowest in summer, which was dominated by Proteobacteria, whereas the highest bacterial diversity presented in high warming regions in winter, which harbored higher proportions of Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. The spatial distribution of bacterial communities showed clear separation especially in summer. Strong correlations were between community compositions and environmental factors, such as salinity, DO, TN, and temperature in summer. Furthermore, remarkable seasonality in bacterial co-occurrence patterns was discovered: the robustness of the bacterial co-occurrence network was promoted in winter, while the complexity and robustness were decreased in summer due to the warming of thermal drainage. These findings reveal the potential factors underpinning the influence of thermal drainage on bacterial community structure, which make it possible to predict the ecological effect of the nuclear power plants by exploring how the microbial assembly is likely to respond to the temperature and other environmental changes.

Extremophiles: the species that evolve and survive under hostile conditions

Extremophiles possess unique cellular and molecular mechanisms to assist, tolerate, and sustain their lives in extreme habitats. These habitats are dominated by one or more extreme physical or chemical parameters that shape existing microbial communities and their cellular and genomic features. The diversity of extremophiles reflects a long list of adaptations over millions of years. Growing research on extremophiles has considerably uncovered and increased our understanding of life and its limits on our planet. Many extremophiles have been greatly explored for their application in various industrial processes. In this review, we focused on the characteristics that microorganisms have acquired to optimally thrive in extreme environments. We have discussed cellular and molecular mechanisms involved in stability at respective extreme conditions like thermophiles, psychrophiles, acidophiles, barophiles, etc., which highlight evolutionary aspects and the significance of extremophiles for the benefit of mankind.

The effects of per- and polyfluoroalkyl substances on environmental and human microorganisms and their potential for bioremediation

Utilised in a variety of consumer products, per- and polyfluoroalkyl substances (PFAS) are major environmental contaminants that accumulate in living organisms due to their highly hydrophobic, lipophobic, heat-resistant, and non-biodegradable properties. This review summarizes their effects on microbial populations in soils, aquatic and biogeochemical systems, and the human microbiome. Specific microbes are insensitive to and even thrive with PFAS contamination, such as Escherichia coli and the Proteobacteria in soil and aquatic environments, while some bacterial species, such as Actinobacteria and Chloroflexi, are sensitive and drop in population. Some bacterial species, in turn, have shown success in PFAS bioremediation, such as Acidimicrobium sp. and Pseudomonas parafulva.

Effect of microbial communities on nitrogen and phosphorus metabolism in rivers with different heavy metal pollution

Small urban and rural rivers usually face heavy metal pollution as a result of urbanization and industrial and agricultural activities. To elucidate the metabolic capacity of microbial communities on nitrogen and phosphorus cycle in river sediments under different heavy metal pollution backgrounds, this study collected samples in situ from two typical rivers, Tiquan River and Mianyuan River, with different heavy metal pollution levels. The microbial community structure and metabolic capacity of nitrogen and phosphorus cycles of sediment microorganisms were analyzed by high-throughput sequencing. The results showed that the major heavy metals in the sediments of the Tiquan River were Zn, Cu, Pb, and Cd with the contents of 103.80, 30.65, 25.95, and 0.44 mg/kg, respectively, while the major heavy metals in the sediments of the Mianyuan River were Cd and Cu with the contents of 0.60 and 27.81 mg/kg, respectively. The dominant bacteria Steroidobacter, Marmoricola, and Bacillus in the sediments of the Tiquan River had positive correlations with Cu, Zn, and Pb while are negatively correlated with Cd. Cd had a positive correlation with Rubrivivax, and Cu had a positive correlation with Gaiella in the sediments of the Mianyuan River. The dominant bacteria in the sediments of the Tiquan River showed strong phosphorus metabolic ability, and the dominant bacteria in the sediments of the Mianyuan River showed strong nitrogen metabolic ability, corresponding to the lower total phosphorus content in the Tiquan River and the higher total nitrogen content in the Mianyuan River. The results of this study showed that resistant bacteria became dominant bacteria due to the stress of heavy metals, and these bacteria showed strong nitrogen and phosphorus metabolic ability. It can provide theoretical support for the pollution prevention and control of small urban and rural rivers and have positive significance for maintaining the healthy development of rivers.

Effects of different botanical oil meal mixed with cow manure organic fertilizers on soil microbial community and function and tobacco yield and quality

Introduction

The continuous application of cow manure in soil for many years leads to the accumulation of heavy metals, pathogenic microorganisms, and antibiotic resistance genes. Therefore, in recent years, cow manure has often been mixed with botanical oil meal as organic fertilizer applied to farmland to improve soil and crop quality. However, the effects of various botanical oil meal and cow manure mixed organic fertilizers on soil microbial composition, community structure, and function, tobacco yield, and quality remain unclear.

Methods

Therefore, we prepared organic manure via solid fermentation by mixing cow manure with different oil meals (soybean meal, rape meal, peanut bran, sesame meal). Then, we studied its effects on soil microbial community structure and function, physicochemical properties, enzyme activities, tobacco yield and quality; then we analyzed the correlations between these factors.

Results and discussion

Compared with cow manure alone, the four kinds of mixed botanical oil meal and cow manure improved the yield and quality of flue-cured tobacco to different degrees. Peanut bran, which significantly improved the soil available phosphorus, available potassium, and NO₃^--N, was the best addition. Compared with cow manure alone, soil fungal diversity was significantly decreased when rape meal or peanut bran was combined with cow manure, while soil bacterial and fungal abundance was significantly increased when rape meal was added compared with soybean meal or peanut bran. The addition of different botanical oil meals significantly enriched the subgroup_7 and Spingomonas bacteria and Chaetomium and Penicillium fungi in the soil. The relative abundances of functional genes of xenobiotics biodegradation and metabolism, soil endophytic fungi, and wood saprotroph functional groups increased. In addition, alkaline phosphatase had the greatest effect on soil microorganisms, while NO₃^--N had the least effect on soil microorganisms. In conclusion, the mixed application of cow manure and botanical oil meal increased the available phosphorus and potassium contents in soil; enriched beneficial microorganisms; promoted the metabolic function of soil microorganisms; increased the yield and quality of tobacco; and improved the soil microecology.

Prokaryotic Community Structure, Abundances, and Potential Ecological Functions in a Mars Analog Salt Lake

Barkol Lake, situated northeast of the Tianshan Mountains, Xinjiang, is a hypersaline lake with abundant sulfate and chloride minerals, which can be a potential analog for microbial saline paleolakes on Mars. The lake water, sediments, and surrounding soils of Barkol Lake were sampled for geochemical analysis and 16S rRNA gene sequencing to investigate the prokaryotic community structure, abundances, interactions, and ecological functions. Results show that (1) prokaryotic community structure differs significantly between biotopes (water, sediment, and soil), with the highest abundances of archaea occurring in water samples and highest prokaryotic diversities in soil samples; (2) archaeal communities are dominated by Halobacterota, Nanoarchaeota, Thermoplasmatota, and Crenarchaeota, while bacterial communities are mainly Proteobacteria, Bacteroidetes, Actinobacteria, Desulfobacterota, Chloroflexi, Gemmatimonadetes, Firmicutes, and Cyanobacteria; (3) the prokaryotic community network for soil is far more complicated and stable than those for water and sediment; (4) soil prokaryotic communities could be significantly affected by environmental factors such as salinity, pH, total sulfur, and Ca²⁺; (5) archaeal communities may play an important role in the nitrogen cycle, while bacterial communities may mainly participate in the sulfur cycle. This study extends the data set of prokaryotic communities for hypersaline environments, which will provide perspectives into identification of the counterparts and help to understand potential microbial interactions and biogeochemical cycles occurring on Mars.

Shouchella tritolerans sp. nov., a facultative anaerobic bacterium isolated from marine sediments

An alkali, salt, and thermo-tolerant strain designated FJAT-45399^T was isolated from marine sediment in Fujian Province, China. Strain FJAT-45399^T was Gram-stain-positive, rod-shaped, and facultatively aerobic. It shared high 16S rRNA gene sequence similarities with the members of the genus Shouchella. Further, the phylogenetic and phylogenomic analysis also suggested strain FJAT-45399^T clustered with the members of the genus Shouchella. Growth of strain FJAT-45399^T was observed at 15-55 °C (optimum 45-50 °C), pH 7.0-13.0 (optimum 9.0) and 0-15% (w/v) NaCl (optimum 2%). It contained MK-7 as the menaquinone. The polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and an unidentified glycolipid (UGL) and lipid (UL). The major fatty acids (> 10%) were C_16:0 (22.8%), iso-C_15:0 (21.3%), and anteiso-C_15:0 (14.0%). The genomic DNA G + C content was 44.5%. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain FJAT-45399^T and the most closely related type strain Shouchella clausii DSM 8716^T (ANI 94.1% and dDDH 55.4%) were both below the cut-off level for species delineation. Based on the above results, strain FJAT-45399^T represents a novel species of the genus Shouchella, for which the name Shouchella tritolerans sp. nov., is proposed. The type strain is FJAT-45399^T (= GDMCC 1.3098^T = JCM 35613^T).

Bacterial diversity in the aquatic system in India based on metagenome analysis-a critical review

Microbial analysis has become one of the most critical areas in aquatic ecology and a crucial component for assessing the contribution of microbes in food web dynamics and biogeochemical processes. Initial research was focused on estimating the abundance and distribution of the microbes using microscopy and culture-based analysis, which are undoubtedly complex tasks. Over the past few decades, microbiologists have endeavored to apply and extend molecular techniques to address pertinent questions related to the function and metabolism of microbes in aquatic ecology. Metagenomics analysis has revolutionized aquatic ecology studies involving the investigation of the genome of a mixed community of organisms in an ecosystem to identify microorganisms, their functionality, and the discovery of novel proteins. This review discusses the metagenomics analysis of bacterial diversity in and around different aquatic systems in India.

To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities

High-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi-sample assembly) and read-based (merged reads and raw data). However, it remains not clear how these different approaches may differ in data analyses and affect result interpretation. In this study, using two typical shotgun metagenome datasets recovered from geographically distant coastal sediments, the performance of different data processing approaches was comparatively investigated from both technical and biological/ecological perspectives. Microbially mediated biogeochemical cycling pathways, including nitrogen cycling, sulfur cycling and B12 biosynthesis, were analyzed. As a result, multi-sample assembly provided the most amount of usable information for targeted functional traits, at a high cost of computational resources and running time. Single-sample assembly and read-based analysis were comparable in obtaining usable information, but the former was much more time- and resource-consuming. Critically, different approaches introduced much stronger variations in microbial profiles than biological differences. However, community-level differences between the two sampling sites could be consistently observed despite the approaches being used. In choosing an appropriate approach, researchers shall balance the trade-offs between multiple factors, including the scientific question, the amount of usable information, computational resources and time cost. This study is expected to provide valuable technical insights and guidelines for the various approaches used for metagenomic data analysis.

Metagenomics reveals biogeochemical processes carried out by sediment microbial communities in a shallow eutrophic freshwater lake

Introduction

As the largest shallow freshwater lake in the North China Plain, Baiyangdian lake is essential for maintaining ecosystem functioning in this highly populated region. Sediments are considered to record the impacts of human activities.

Methods

The abundance, diversity and metabolic pathways of microbial communities in sediments were studied by metagenomic approach to reveal patterns and mechanism of C, N, P and S cycling under the threat of lake eutrophication.

Results

Many genera, with plural genes encoding key enzymes involved in genes, belonging to Proteobacteria and Actinobacteria which were the most main phylum in bacterial community of Baiyangdian sediment were involved in C, N, S, P cycling processes, such as Nocardioides (Actinobacteria), Thiobacillus, Nitrosomonas, Rhodoplanes and Sulfuricaulis (Proteobacteria).For instance, the abundance of Nocardioides were positively correlated to TN, EC, SOC and N/P ratio in pathways of phytase, regulation of phosphate starvation, dissimilatory sulfate reduction and oxidation, assimilatory sulfate reduction, assimilatory nitrate reduction and reductive tricarboxylic acid (rTCA) cycle. Many key genes in C, N, P, S cycling were closely related to the reductive citrate cycle. A complete while weaker sulfur cycle between SO₄ ^2- and HS^- might occur in Baiyangdian lake sediments compared to C fixation and N cycling. In addition, dissimilatory nitrate reduction to ammonia was determined to co-occur with denitrification. Methanogenesis was the main pathway of methane metabolism and the reductive citrate cycle was accounted for the highest proportion of C fixation processes. The abundance of pathways of assimilatory nitrate reduction, denitrification and dissimilatory nitrate reduction of nitrogen cycling in sediments with higher TN content was higher than those with lower TN content. Besides, Nocardioides with plural genes encoding key enzymes involved in nasAB and nirBD gene were involved in these pathways.

Discussion

Nocardioides involved in the processes of assimilatory nitrate reduction, denitrification and dissimilatory nitrate reduction of nitrogen cycling may have important effects on nitrogen transformation.

Response of soil microbial communities and rice yield to nitrogen reduction with green manure application in karst paddy areas

Fertilizer application practices are one of the major challenges facing agroecology. The agrobenefits of combined application of green manure and chemical fertilizers, and the potential of green manure to replace chemical fertilizers are now well documented. However, little is known about the impact of fertilization practices on microbial communities and tice yield. In this study, the diversity of bacterial and fungal communities, symbiotic networks and their relationship with soil function were analyzed in five fertilization treatments (N: 100% nitrogen fertilizer alone; M: green manure alone; MN₆₀: green manure couple with 60% nitrogen fertilizer, MN₈₀: green manure couple with 80% nitrogen fertilizer; and MN₁₀₀: green manure couple with 100% nitrogen fertilizer). First, early rice yield was significantly higher by 12.6% in MN₁₀₀ treatment in 2021 compared with N. Secondly, soil bacterial diversity showed an increasing trend with increasing N fertilizer application after green manure input, however, the opposite was true for fungal diversity. Microbial interaction analysis showed that different fertilizer applications changed soil microbial network complexity and fertilizer-induced changes in soil microbial interactions were closely related to soil environmental changes. Random forest models further predicted the importance of soil environment, microorganisms and rice yield. Overall, nitrogen fertilizer green manure altered rice yield due to its effects on soil environment and microbial communities. In the case of combined green manure and N fertilizer application, bacteria and fungi showed different responses to fertilization method, and the full amount of N fertilizer in combination with green manure reduced the complexity of soil microbial network. In contrast, for more ecologically sensitive karst areas, we recommend fertilization practices with reduced N by 20-40% for rice production. Graphical Abstract.

Cladophora can mitigate the shock of glyphosate-containing wastewater on constructed wetlands coupled with microbial fuel cells

This study investigated the performance of constructed wetlands coupled with microbial fuel cells (CW-MFCs) treating agricultural wastewater containing glyphosate (N-phosphonomethyl glycine, PMG), and the use of Cladophora as a cathode plant in this system. Ten devices were divided into Cladophora groups (CGs) and no Cladophora groups (NGs), with five PMG concentrations (0, 10, 25, 50, and 100 mg/L). PMG removal efficiency significantly decreased with increasing PMG (P < 0.01) and was higher in CG devices than in NG devices at low PMG concentrations (<50 mg/L). The removal efficiency of chemical oxygen demand (COD) and NH₄⁺ in CGs was significantly higher than in NGs (P < 0.01). The highest power densities of 6.37 (CGs) and 6.26 mW/m² (NGs) were obtained at 50 mg/L PMG, and the average voltage was significantly higher in CGs than in NGs (p < 0.01). Moreover, PMG had a negative effect on the enrichment of electrochemically active bacteria, but Cladophora could mitigate this effect. The abundance of the resistance gene epsps was stabilized; The phnJ gene increased with increasing PMG in NGs and was downregulated at high PMG concentration in CGs, indicating better microbial adaptation to PMG in CGs throughout the experiment.

Enhanced removal of sulfur-containing organic pollutants from actual wastewater by biofilm reactor: Insights of sulfur transformation and bacterial metabolic traits

Sulfur-containing organic pollutants in wastewater could threaten human health due to their high malodor and toxicity, and their conversion processes are more complex than inorganic sulfur compounds. Membrane aerated biofilm reactor (MABR), as a novel and environmentally-friendly biofilm-based technology, is able to remove inorganic sulfur in synthetic wastewater. However, it is unknown how sulfur-containing organic pollutants in actual wastewater are transformed in MABR system. This work demonstrated the feasibility of MABR to eliminate sulfur-containing organic pollutants in actual wastewater, and the removal efficiency could be reached at approximately 100%. Meanwhile, over 70% of sulfur-containing organic contaminants were transformed to SO₄^2- during the long-term operation. Further analysis indicated that the functional bacteria that participated in sulfur transformation and carbohydrates degradation (e.g., Chujaibacter, Microscillaceaesp., and Thiobacillus) were evidently enriched when treating actual wastewater. Moreover, the critical metabolic pathways (e.g., sulfur metabolism, glycolysis metabolism, and pyruvate metabolism), and the corresponding genetic expressions (e.g., nrrA, tauA, tauC, sorA, and SUOX) were evidently up-regulated during long-term operation, which was beneficial for the transformation of sulfur-containing organic pollutants in actual wastewater by MABR. This work would expand the application of MABR for treating the actual sulfur-containing organic wastewater and provide an in-depth understanding of the organic sulfur transformation in MABR.

Aerobic granular sludge cultivated from Fe-loaded activated carbon as carrier working low-strength wastewater conditions by bioreactor

This study proposes a new method to promote the granulation process while accelerating the degradation efficiency of nutrients. The new strategy could involve preparing Fe-loaded activated carbon (FAC) before start-up of granular cultivation and then cultivating the process of aerobic granular sludge (AGS) with such materials. In addition, this experiment could further comprehend how the preparation and characteristics of FAC affect the formation and properties of AGS. The conclusions showed that compared with the control, FAC enhanced the sedimentation performance and significant removal efficiency. Meanwhile, the values of protein (PN) and polysaccharide (PS) also increased significantly in the addition of FAC, indicating the production of substances were induced by FAC. Molecular biology methods indicated that the rapid production of granulation and removal of nutrients were considered as the abundance of various microbes and denitrifying bacteria at the addition of FAC. This research showed that the presence of FAC is a useful strategy for the initiation of sludge particle formation to promote the treatment of wastewater, containing COD and NH₄⁺ at about 150-100 and 30 mg L^-1.

Responses of Cyanobacterial Crusts and Microbial Communities to Extreme Environments of the Stratosphere

How microbial communities respond to extreme conditions in the stratosphere remains unclear. To test this effect, cyanobacterial crusts collected from Tengger Desert were mounted to high balloons and briefly exposed (140 min) to high UV irradiation and low temperature in the stratosphere at an altitude of 32 km. Freezing and thawing treatments were simulated in the laboratory in terms of the temperature fluctuations during flight. Microbial community composition was characterized by sequencing at the level of DNA and RNA. After exposure to the stratosphere, the RNA relative abundances of Kallotenue and Longimicrobium increased by about 2-fold, while those of several dominant cyanobacteria genera changed slightly. The RNA relative abundances of various taxa declined after freezing, but increased after thawing, whereas cyanobacteria exhibited an opposite change trend. The DNA and RNA relative abundances of Nitrososphaeraceae were increased by 1.4~2.3-fold after exposure to the stratosphere or freezing. Exposure to stratospheric environmental conditions had little impact on the total antioxidant capacity, photosynthetic pigment content, and photosynthetic rate, but significantly increased the content of exopolysaccharides by 16%. The three treatments (stratospheric exposure, freezing, and thawing) increased significantly the activities of N-acetyl-β-D-glucosidase (26~30%) and β-glucosidase (14~126%). Our results indicated cyanobacterial crust communities can tolerate exposure to the stratosphere. In the defense process, extracellular organic carbon degradation and transformation play an important role. This study makes the first attempt to explore the response of microbial communities of cyanobacterial crusts to a Mars-like stratospheric extreme environment, which provides a new perspective for studying the space biology of earth communities.