Genomic analysis of Chthonomonas calidirosea, the first sequenced isolate of the phylum Armatimonadetes

Relationships between radiation, wildfire and the soil microbial communities in the Chornobyl Exclusion Zone

There is considerable uncertainty regarding radiation's effects on biodiversity in natural complex ecosystems typically subjected to multiple environmental disturbances and stresses. In this study we characterised the relationships between soil microbial communities and estimated total absorbed dose rates to bacteria, grassy vegetation and trees in the Red Forest region of the Chornobyl Exclusion Zone. Samples were taken from sites of contrasting ecological histories and along burn and no burn areas following a wildfire. Estimated total absorbed dose rates to bacteria reached levels one order of magnitude higher than those known to affect bacteria in laboratory studies. Sites with harsher ecological conditions, notably acidic pH and low soil moisture, tended to have higher radiation contamination levels. No relationship between the effects of fire and radiation were observed. Microbial groups that correlated with high radiation sites were mostly classified to taxa associated with high environmental stress habitats or stress resistance traits. Distance-based linear models and co-occurrence analysis revealed that the effects of radiation on the soil microbiome were minimal. Hence, the association between high radiation sites and specific microbial groups is more likely a result of the harsher ecological conditions in these sites, rather than due to radiation itself. In this study, we provide a starting point for understanding the relationship between soil microbial communities and estimated total absorbed radiation dose rates to different components of an ecosystem highly contaminated with radiation. Our results suggest that soil microbiomes adapted to natural soil conditions are more likely to be resistant to ionising radiation than expected from laboratory studies, which demonstrates the importance of assessing the impact of ionising radiation on soil microbial communities under field conditions.

Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation

BACKGROUND

Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58-74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism.

RESULTS

Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures.

CONCLUSIONS

This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities.

Fecal and oral microbiome analysis of snakes from China reveals a novel natural emerging disease reservoir

Introduction

The gastrointestinal tract and oral cavity of animal species harbor complex microbial communities, the composition of which is indicative of the behavior, co-evolution, diet, and immune system of the host.

Methods

This study investigated the microbial composition in snakes from varying altitudinal ranges by assessing the fecal and oral bacterial communities in Protobothrops mucrosquamatus, Elaphe dione, and Gloydius angusticeps from Sichuan Province, China, using metagenomic sequencing.

Results and discussion

It was revealed that Bacteroidetes, Proteobacteria, Firmicutes, and Fusobacteria were the core microbial phyla in fecal samples across all three species, while Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes were the core microbial phyla in oral samples across all three species. Notably, the dominance of Armatimonadetes was documented for the first time in the feces of all three species. Comparative analysis of the microbiomes of the three species indicated distinct microbiological profiles between snakes living at low- and high-altitude regions. Furthermore, 12 to 17 and 22 to 31 bacterial pathogens were detected in the oral and fecal samples, respectively, suggesting that snakes may serve as a novel reservoir for emerging diseases. Overall, this study provides a comparative analysis of the fecal and oral microbiomes in three snake species. Future investigations are anticipated to further elucidate the influence of age, genetics, behavior, diet, environment, ecology, and evolution on the gut and oral microbial communities of snakes.

Gut microbiota and metabolites exhibit different profiles after very-low-caloric restriction in patients with type 2 diabetes

Background and aims

To investigate the effect of short-term very-low-calorie restriction (VLCR) on metabolism in patients with type 2 diabetes (T2D), and elucidate the molecular mechanism through analyses on gut microbiota and small-molecule metabolites.

Methods

Fourteen T2D patients were hospitalized to receive VLCR (300-600 kcal/d) for 9 days. BMI, BP, and HR were taken before and after VLCR. Levels of blood lipids, fasting insulin, FBG, and 2h PBG were assessed. The microbial diversity in feces was detected by 16S rDNA high-throughput sequencing technology, and small-molecule metabolites in plasma and feces by untargeted metabolomics technology.

Results

After VLCR, BW, BMI, WC, BP, and levels of FBG and 2h PBG, insulin, HOMA-IR, and triglyceride decreased significantly in T2D patients (P<0.05). There was no significant change in the α-diversity of fecal microbiota, but the abundance of Bacteroidetes increased significantly, and the Firmicutes/Bacteroidetes ratio decreased significantly from 11.79 to 4.20. Parabacteroides distasonis showed an abundance having increased most prominently after VLCR treatment. Plasma level of amino acid metabolite L-arginine increased significantly. Plasma levels of three lipid metabolites, PC (14:0/20:4 [8Z, 11Z, 14Z, 17Z]), LysoPC (16:1 [9Z]) and LysoPC (18:1 [11Z]), were significantly reduced. Fecal levels of lipid metabolite LysoPC (18:1 [11Z]) and bile acid metabolite glycholic acid were significantly decreased.

Conclusion

In T2DM patients, VLCR can considerably reduce body weight and improve glucose and lipid metabolism without causing severe side effects. LysoPC (18:1 [11Z]) and Parabacteroides distasonis showed the most obvious difference after VLCR, which could be the indicators for VLCR in T2D.

Effect and mechanism of NaHS on tobacco bacterial wilt caused by Ralstonia solanacearum

Since its discovery as a third unique gaseous signal molecule, hydrogen sulfide (H₂S) has been extensively employed to resist stress and control pathogens. Nevertheless, whether H₂S can prevent tobacco bacterial wilt is unknown yet. We evaluated the impacts of the H₂S donor sodium hydrosulfide (NaHS) on the antibacterial activity, morphology, biofilm, and transcriptome of R. solanacearum to understand the effect and mechanism of NaHS on tobacco bacterial wilt. In vitro, NaHS significantly inhibited the growth of Ralstonia solanacearum and obviously altered its cell morphology. Additionally, NaHS significantly inhibited the biofilm formation and swarming motility of R. solanacearum, and reduced the population of R. solanacearum invading tobacco roots. In field experiments, the application of NaHS dramatically decreased the disease incidence and index of tobacco bacterial wilt, with a control efficiency of up to 89.49%. The application of NaHS also influenced the diversity and structure of the soil microbial community. Furthermore, NaHS markedly increased the relative abundances of beneficial microorganisms, which helps prevent tobacco bacterial wilt. These findings highlight NaHS's potential and efficacy as a powerful antibacterial agent for preventing tobacco bacterial wilt caused by R. solanacearum.

Repeated hydrogen peroxide dosing briefly reduces cyanobacterial blooms and microcystin while increasing fecal bacteria indicators in a eutrophic pond

This study explored the effects of H₂O₂ on Cyanobacteria and non-target microbes using fluorometry, microscopy, flow cytometry, and high throughput DNA sequencing of the 16S rRNA gene during a series of mesocosm and whole-ecosystem experiments in a eutrophic pond in NY, USA. The addition of H₂O₂ (8 mg/L) significantly reduced Cyanobacteria concentrations during a majority of experiments (66%; 6 of 9) and significantly increased eukaryotic green and unicellular brown algae in 78% and 45% of experiments, respectively. While heterotrophic bacteria declined significantly following H₂O₂ addition in all experiments, bacteria indicative of potential fecal contamination (Escherichia coli, Enterococcus, fecal coliform bacteria) consistently and significantly increased in response to H₂O₂, evidencing a form of 'pollution swapping'. H₂O₂ more effectively reduced Cyanobacteria in enclosed mesocosms compared to whole-ecosystem applications. Ten whole-pond H₂O₂ applications over a two-year period temporarily reduced cyanobacterial levels but never reduced concentrations below bloom thresholds and populations always rebounded in two weeks or less. The bacterial phyla of Cyanobacteria, Actinobacteria, and Planctomycetes were the most negatively impacted by H₂O₂. Microcystis was always reduced by H₂O₂, as was the toxin microcystin, but Microcystis remained dominant even after repeated H₂O₂ treatments. Although H₂O₂ favored the growth of eukaryotic algae over potentially harmful Cyanobacteria, the inability of H₂O₂ to end cyanobacterial blooms in this eutrophic waterbody suggests it is a non-ideal mitigation approach in high biomass ecosystems and should be used judiciously due to potential negative impacts on non-target organisms and promotion of bacteria indicative of fecal contamination.

Microbial carbon, sulfur, iron, and nitrogen cycling linked to the potential remediation of a meromictic acidic pit lake

Cueva de la Mora is a permanently stratified acidic pit lake and a model system for extreme acid mine drainage (AMD) studies. Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling. We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline. The chemocline had activity for iron(II) oxidation carried out by populations of Ca. Acidulodesulfobacterium, Ferrovum, Leptospirillium, and Armatimonadetes. Predicted activity for iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria. Activity for dissimilatory nitrogen cycling including nitrogen fixation and nitrate reduction was primarily predicted in the chemocline. Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer. Abundant sulfate-reducing Desulfomonile and Ca. Acidulodesulfobacterium populations were active in the chemocline. In the deep layer, uncultured populations from the bacterial phyla Actinobacteria, Chloroflexi, and Nitrospirae contributed to both sulfate reduction and sulfide oxidation. Based on this information we evaluated the potential for sulfide mineral precipitation in the deep layer as a tool for remediation. We argue that sulfide precipitation is not limited by microbial genetic potential but rather by the quantity and quality of organic carbon reaching the deep layer as well as by oxygen additions to the groundwater enabling sulfur oxidation. Addition of organic carbon and elemental sulfur should stimulate sulfate reduction and limit reoxidation of sulfide minerals.

A potential network structure of symbiotic bacteria involved in carbon and nitrogen metabolism of wood-utilizing insect larvae

Effective biological utilization of wood biomass is necessary worldwide. Since several insect larvae can use wood biomass as a nutrient source, studies on their digestive microbial structures are expected to reveal a novel rule underlying wood biomass processing. Here, structural inferences for inhabitant bacteria involved in carbon and nitrogen metabolism for beetle larvae, an insect model, were performed to explore the potential rules. Bacterial analysis of larval feces showed enrichment of the phyla Chroloflexi, Gemmatimonadetes, and Planctomycetes, and the genera Bradyrhizobium, Chonella, Corallococcus, Gemmata, Hyphomicrobium, Lutibacterium, Paenibacillus, and Rhodoplanes, as bacteria potential involved in plant growth promotion, nitrogen cycle modulation, and/or environmental protection. The fecal abundances of these bacteria were not necessarily positively correlated with their abundances in the habitat, indicating that they were selectively enriched in the feces of the larvae. Correlation and association analyses predicted that common fecal bacteria might affect carbon and nitrogen metabolism. Based on these hypotheses, structural equation modeling (SEM) statistically estimated that inhabitant bacterial groups involved in carbon and nitrogen metabolism were composed of the phylum Gemmatimonadetes and Planctomycetes, and the genera Bradyrhizobium, Corallococcus, Gemmata, and Paenibacillus, which were among the fecal-enriched bacteria. Nevertheless, the selected common bacteria, i.e., the phyla Acidobacteria, Armatimonadetes, and Bacteroidetes and the genera Candidatus Solibacter, Devosia, Fimbriimonas, Gemmatimonas Opitutus, Sphingobium, and Methanobacterium, were necessary to obtain good fit indices in the SEM. In addition, the composition of the bacterial groups differed depending upon metabolic targets, carbon and nitrogen, and their stable isotopes, δ¹³C and δ¹⁵N, respectively. Thus, the statistically derived causal structural models highlighted that the larval fecal-enriched bacteria and common symbiotic bacteria might selectively play a role in wood biomass carbon and nitrogen metabolism. This information could confer a new perspective that helps us use wood biomass more efficiently and might stimulate innovation in environmental industries in the future.

One-step preparation of cell-free ATP regeneration module based on non-oxidative glycolysis using thermophilic enzymes

Adenosine triphosphate (ATP) is an essential cofactor for energy-dependent enzymatic reactions that occur during in vitro biochemical conversion. Recently, an enzyme cascade based on non-oxidative glycolysis, which uses starch and orthophosphate as energy and phosphate sources, respectively, for the regeneration of ATP from adenosine diphosphate, has been developed (Wei et. al., ChemCatChem 2018 , 10 , 5597-5601). However, the 12 enzymes required for this system hampered its practical usability and further testing potential. Here, we addressed this issue by constructing co-expression vectors for the simultaneous gene expression of the 12 enzymes in a single expression strain. All enzymes were sourced from (hyper)thermophiles, which enabled a one-step purification via a heat-treatment process. We showed that the combination of the two enabled the ATP regeneration system to function in a single recombinant Escherichia coli strain. Additionally, this work provides a strategy to rationally design and control proteins expression levels in the co-expression vectors.

Grazing Changed Plant Community Composition and Reduced Stochasticity of Soil Microbial Community Assembly of Alpine Grasslands on the Qinghai-Tibetan Plateau

Grazing is a substantial threat to the sustainability of grassland ecosystems, while it is uncertain about the variety of plant and soil microbial community and the linkages between them limit the comprehensive understanding of grazing ecology. We conducted an experiment on the effects of the grazing regimes rotational grazing (RG), continuous grazing (CG), and grazing exclusion (GE) on an alpine meadow in Qinghai-Tibetan Plateau. The differences of plant community composition, soil microbial community assembly mechanism, and taxonomic and functional composition between grazing regimes were examined, and the relationship between plant species and the soil microbes was assessed by constructing a co-occurrence network. The results showed that the plant community composition varied with the grazing regimes, while the soil microbial community composition did not vary with the grazing regimes. The soil bacterial functional composition was similar under RG and CG, while the soil fungal functional composition was similar under GE and RG. The soil microbial community under all grazing regimes was assembled mainly according to stochastic rather than deterministic mechanisms, and RG and CG reduced the relative importance of the stochastic ratio. At the microbial phylum level, CG and GE increased the relative abundance of Acidobacteria and Armatimonadetes and CG and RG increased the relative abundance of Elusimicrobia. In the network of plant species and soil microbial classes, plants and bacteria themselves were mainly positively linked (symbiosis and promotion), while plants and soil microbes were mainly negatively linked (competition). There were five microbial generalists in the network, which connected with many microbes, and four showed no difference in their abundance among the grazing regimes. Overall, the stable key microbes in the network and the fact that many of the plants are unconnected with microbes weakened the impact of grazing-induced changes in the plant community on soil microbes, probably resulting in the stable soil microbial community composition. Moreover, there was still a dominant and tolerant plant species, Kobresia pygmaea, that connected the plant and microbial communities, implying that the dominant plant species not only played a crucial role in the plant community but also acted as a bridge between the plants and soil microbes; thus, its tolerance and dominance might stabilize the soil microbial community.

Thermophiles and carbohydrate-active enzymes (CAZymes) in biofilm microbial consortia that decompose lignocellulosic plant litters at high temperatures

The SKY hot spring is a unique site filled with a thick layer of plant litter. With the advancement of next-generation sequencing, it is now possible to mine many new biocatalyst sequences. In this study, we aimed to (i) identify the metataxonomic of prokaryotes and eukaryotes in microbial mats using 16S and 18S rRNA markers, (ii) and explore carbohydrate degrading enzymes (CAZymes) that have a high potential for future applications. Green microbial mat, predominantly photosynthetic bacteria, was attached to submerged or floating leaves litter. At the spring head, the sediment mixture consisted of plant debris, predominantly brownish-reddish gelatinous microbial mat, pale tan biofilm, and grey-white filament biofilm. The population in the spring head had a higher percentage of archaea and hyperthermophiles than the green mat. Concurrently, we cataloged nearly 10,000 sequences of CAZymes in both green and brown biofilms using the shotgun metagenomic sequencing approach. These sequences include β-glucosidase, cellulase, xylanase, α-N-arabinofuranosidase, α-l-arabinofuranosidase, and other CAZymes. In conclusion, this work elucidated that SKY is a unique hot spring due to its rich lignocellulosic material, often absent in other hot springs. The data collected from this study serves as a repository of new thermostable macromolecules, in particular families of glycoside hydrolases.

A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial Systems

The Arctic environment is particularly affected by global warming, and a clear trend of the ice retreat is observed worldwide. In proglacial systems, the newly exposed terrain represents different environmental and nutrient conditions compared to later soil stages. Therefore, proglacial systems show several environmental gradients along the soil succession where microorganisms are active protagonists of the soil and carbon pool formation through nitrogen fixation and rock weathering. We studied the microbial succession of three Arctic proglacial systems located in Svalbard (Midtre Lovénbreen), Sweden (Storglaciären), and Greenland (foreland close to Kangerlussuaq). We analyzed 65 whole shotgun metagenomic soil samples for a total of more than 400 Gb of sequencing data. Microbial succession showed common trends typical of proglacial systems with increasing diversity observed along the forefield chronosequence. Microbial trends were explained by the distance from the ice edge in the Midtre Lovénbreen and Storglaciären forefields and by total nitrogen (TN) and total organic carbon (TOC) in the Greenland proglacial system. Furthermore, we focused specifically on genes associated with nitrogen fixation and biotic rock weathering processes, such as nitrogenase genes, obcA genes, and genes involved in cyanide and siderophore synthesis and transport. Whereas we confirmed the presence of these genes in known nitrogen-fixing and/or rock weathering organisms (e.g., Nostoc, Burkholderia), in this study, we also detected organisms that, even if often found in soil and proglacial systems, have never been related to nitrogen-fixing or rock weathering processes before (e.g., Fimbriiglobus, Streptomyces). The different genera showed different gene trends within and among the studied systems, indicating a community constituted by a plurality of organisms involved in nitrogen fixation and biotic rock weathering, and where the latter were driven by different organisms at different soil succession stages.

Integrated biocontrol of tobacco bacterial wilt by antagonistic bacteria and marigold

Tobacco bacterial wilt (TBW) is seriously damages the growth of tobacco. There is an urgent need to find a safer and more effective measure to control TBW. In this study, B. amyloliquefaciens ZM9 and marigold powder were applied to the tobacco roots alone or in combination, and the potential inhibition of TBW was assessed. On the other hand, the effects of these treatments on soil physicochemical properties, rhizosphere microbial community and soil metabolites were also evaluated. The results showed that the application of B. amyloliquefaciens ZM9 or marigold powder alone significantly reduced the abundance of R. solanacearum in rhizosphere soil, while the integrated treatment showed the strongest inhibitory effect. Moreover, the integrated treatment can inhibit the secretion of chemoattractants, and affect the change of rhizosphere soil microbial composition. In conclusion, the combination of antagonistic bacteria agent B. amyloliquefaciens ZM9 with marigold powder can enhance the suppression of TBW. Furthermore, B. amyloliquefaciens ZM9 and marigold have synergistic effects on suppressing TBW by regulation soil physicochemical properties, soil metabolites and microbial structure. This study provide a promising strategy for TBW control by integrated applying of B. amyloliquefaciens ZM9 and marigold powder.

Effects of integrated biocontrol on bacterial wilt and rhizosphere bacterial community of tobacco

Bacterial wilt as a soil-borne disease was caused by Ralstonia solanacearum, and seriously damages the growth of tobacco. Integrated biocontrol method was explored to control bacterial wilt. Nevertheless, the long-term effects of the integrated biocontrol method on soil bacterial community, soil physicochemical properties and the incidence of bacterial wilt are not well understood. In this study, B. amyoliquefaciens ZM9, calcium cyanamide and rice bran were applied to tobacco fields in different ways. The disease index and incidence of tobacco bacterial wilt (TBW), soil physicochemical properties, colonization ability of B. amyoliquefaciens ZM9, and rhizopshere bacterial community were investigated. The results showed that the integrated application of B. amyoliquefaciens ZM9, rice bran and calcium cyanamide had the highest control efficiency of TBW and bacteria community diversity. Additionally, the integrated biocontrol method could improve the colonization ability of B. amyoliquefaciens ZM9. Furthermore, the integrated biocontrol method could effectively suppress TBW by regulating soil physicochemical properties, promoting beneficial bacteria and antagonistic bacteria of rhizopshere soil. This strategy has prospect of overcoming the defects in application of a single antagonistic bacteria and provides new insights to understand how to improve the colonization capacity of antagonistic bacteria and control efficacy for TBW.

Microbial Life in the Deep Subsurface Aquifer Illuminated by Metagenomics

To get insights into microbial diversity and biogeochemical processes in the terrestrial deep subsurface aquifer, we sequenced the metagenome of artesian water collected at a 2.8 km deep oil exploration borehole 5P in Western Siberia, Russia. We obtained 71 metagenome-assembled genomes (MAGs), altogether comprising 93% of the metagenome. Methanogenic archaea accounted for about 20% of the community and mostly belonged to hydrogenotrophic Methanobacteriaceae; acetoclastic and methylotrophic lineages were less abundant. ANME archaea were not found. The most numerous bacteria were the Firmicutes, Ignavibacteriae, Deltaproteobacteria, Chloroflexi, and Armatimonadetes. Most of the community was composed of anaerobic heterotrophs. Only six MAGs belonged to sulfate reducers. These MAGs accounted for 5% of the metagenome and were assigned to the Firmicutes, Deltaproteobacteria, Candidatus Kapabacteria, and Nitrospirae. Organotrophic bacteria carrying cytochrome c oxidase genes and presumably capable of aerobic respiration mostly belonged to the Chloroflexi, Ignavibacteriae, and Armatimonadetes. They accounted for 13% of the community. The first complete closed genomes were obtained for members of the Ignavibacteriae SJA-28 lineage and the candidate phylum Kapabacteria. Metabolic reconstruction of the SJA-28 bacterium, designated Candidatus Tepidiaquacella proteinivora, predicted that it is an anaerobe growing on proteinaceous substrates by fermentation or anaerobic respiration. The Ca. Kapabacteria genome contained both the sulfate reduction pathway and cytochrome c oxidase. Presumably, the availability of buried organic matter of Mesozoic marine sediments, long-term recharge of the aquifer with meteoric waters and its spatial heterogeneity provided the conditions for the development of microbial communities, taxonomically and functionally more diverse than those found in oligotrophic underground ecosystems.

Biomarker Profiling of Microbial Mats in the Geothermal Band of Cerro Caliente, Deception Island (Antarctica): Life at the Edge of Heat and Cold

Substrate-atmosphere interfaces in Antarctic geothermal environments are hot-cold regions that constitute thin habitable niches for microorganisms with possible counterparts in ancient Mars. Cerro Caliente hill in Deception Island (active volcano in the South Shetland Islands) is affected by ascending hydrothermal fluids that form a band of warm substrates buffered by low air temperatures. We investigated the influence of temperature on the community structure and metabolism of three microbial mats collected along the geothermal band of Cerro Caliente registering 88°C, 8°C, and 2°C at the time of collection. High-throughput sequencing of small subunit ribosomal ribonucleic acid (SSU rRNA) genes and Life Detector Chip (LDChip) microarray immunoassays revealed different bacterial, archaeal, and eukaryotic composition in the three mats. The mat at 88°C showed the less diverse microbial community and a higher proportion of thermophiles (e.g., Thermales). In contrast, microbial communities in the mats at 2°C and 8°C showed relatively higher diversity and higher proportion of psychrophiles (e.g., Flavobacteriales). Despite this overall association, similar microbial structures at the phylum level (particularly the presence of Cyanobacteria) and certain hot- and cold-tolerant microorganisms were identified in the three mats. Daily thermal oscillations recorded in the substrate over the year (4.5-76°C) may explain the coexistence of microbial fingerprints with different thermal tolerances. Stable isotope composition also revealed metabolic differences among the microbial mats. Carbon isotopic ratios suggested the Calvin-Benson-Bassham cycle as the major pathway for carbon dioxide fixation in the mats at 2°C and 8°C, and the reductive tricarboxylic acid cycle and/or the 3-hydroxypropionate bicycle for the mat at 88°C, indicating different metabolisms as a function of the prevailing temperature of each mat. The comprehensive biomarker profile on the three microbial mats from Cerro Caliente contributes to unravel the diversity, composition, and metabolism in geothermal polar sites and highlights the relevance of geothermal-cold environments to create habitable niches with interest in other planetary environments.

Biochar amendment controlled bacterial wilt through changing soil chemical properties and microbial community

Long-term continuous cropping has led to epidemic of bacterial wilt disease in Southern China. Bacterial wilt disease is caused by Ralstonia solanacearum and difficult to control. In order to control bacterial wilt, rice hull biochar was applied to soil with different doses (0, 7.5, 15, 30 and 45 t ha^-1) in a field trial. After three years, the influence of biochar on soil properties, incidence of bacterial wilt and microbial community were characterized. Biochar amendment significantly suppressed bacterial wilt through changing soil chemical properties and microbial composition. Compared with control, disease incidence and index of biochar amendments (7.5, 15, 30, and 45 t ha^-1) significantly decreased. Disease incidence and index of biochar amendment (15 t ha^-1) were the lowest. Compared to the unamended control, contents of soil organic matter in biochar amendments (15, 30 t ha^-1), available nitrogen in biochar amendment (15 t ha^-1), and urease activity in biochar amendments (7.5, 15 t ha^-1) significantly increased. Biochar amendments (15, 30, and 45 t ha^-1) increased the relative abundances of potential beneficial bacteria (Aeromicrobium, Bacillus, Bradyrhizobium, Burkholderia, Chlorochromatium, Chthoniobacter, Corynebacterium, Geobacillus, Leptospirillum, Marisediminicola, Microvirga, Pseudoxanthomonas, Telmatobacter). Biochar amendments (7.5, 30, and 45 t ha^-1) reduced the relative abundances of denitrifying bacteria (Noviherbaspirillum, Reyranella, Thermus). Biochar amendments (7.5, 15, and 45 t ha^-1) significantly decreased pathogen Ralstonia abundance. Overall, application of biochar effectively controlled bacterial wilt through sequestering more carbon and nitrogen, enriching specific beneficial bacteria and decreasing pathogen abundance. This study revealed the potential of biochar in control of bacterial wilt.

Response of soil bacterial community structure to different reclamation years of abandoned salinized farmland in arid China

In recent years, understanding the impact of reclamation of abandoned salinized field on microbial community structure is of great importance for ecosystem restoration in arid regions. The aim of this work was to investigate the effects of reclamation years on soil properties, bacterial community composition and diversity based on field sampling and llumina MiSeq sequencing. The five reclamation years are: unreclaimed salinized and reclaimed (1, 5, 10, and 15 years) fields. The results showed soil properties are significantly altered by abandoned salinized field. In particular, reclamation significantly decreased soil electrical conductivity, Cl^-, SO₄^2-, Na⁺, and Ca²⁺, during 5 years of reclamation. In addition, reclamation increased the richness and diversity of the bacterial community, except for the 1-year field soils. There was a large difference in the abundant bacterial phyla in 1-year field soils compared with other field soils. Proteobacteria were the most abundant in all of the field soils. Principal coordinates analysis showed that the abandoned and 1-year field soils exhibited specific differences in bacterial community structures compared with other field soils. Statistical analyses showed that available phosphorus, SO₄^2-, Mg²⁺, and Ca²⁺ were the main physicochemical properties affecting the soil bacterial communities. Overall, reclamation improved soil physicochemical properties and altered the structure and composition of soil bacterial communities compared with unreclaimed salinized soil.

Effects of Various Carbon Nanotubes on Soil Bacterial Community Composition and Structure

Carbon nanotubes (CNTs) have huge industrial potential, and their environmental impacts need to be evaluated. Knowledge of CNT impacts on soil microbial communities is still limited. To address this knowledge gap, we systematically examined dynamic effects of one type of single-walled carbon nanotubes (SWs) and three multiwalled carbon nanotubes (MWs) with different outer diameters on the soil bacterial community in an agricultural soil over 56 days. The results showed that SWs differently affected soil bacterial abundance, diversity, and composition as compared to MWs. The differences could have resulted from the materials' distinct physical structure and surface composition, which in turn affected their bioavailability in soil. For certain treatments, soil bacterial diversity and the relative abundance of certain predominant phyla were correlated with their exposure duration. However, many phyla recovered to their initial relative abundance within 56 days, reflecting resilience of the soil bacterial community in response to CNT-induced disturbance. Further analysis at the genus level showed differential tolerance to MWs, as well as size- and dose-dependent tolerance among bacterial genera. Predictive functional profiling showed that while CNTs initially caused fluctuations in microbial community function, community function largely converged across all treatments by the end of the 56 day exposure.

Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

Delignification, or lignin-modification, facilitates the decomposition of lignocellulose in woody plant biomass. The extant diversity of lignin-degrading bacteria and fungi is underestimated by culture-dependent methods, limiting our understanding of the functional and ecological traits of decomposers populations. Here, we describe the use of stable isotope probing (SIP) coupled with amplicon and shotgun metagenomics to identify and characterize the functional attributes of lignin, cellulose and hemicellulose-degrading fungi and bacteria in coniferous forest soils from across North America. We tested the extent to which catabolic genes partitioned among different decomposer taxa; the relative roles of bacteria and fungi, and whether taxa or catabolic genes correlated with variation in lignocellulolytic activity, measured as the total assimilation of ¹³C-label into DNA and phospholipid fatty acids. We found high overall bacterial degradation of our model lignin substrate, particularly by gram-negative bacteria (Comamonadaceae and Caulobacteraceae), while fungi were more prominent in cellulose-degradation. Very few taxa incorporated ¹³C-label from more than one lignocellulosic polymer, suggesting specialization among decomposers. Collectively, members of Caulobacteraceae could degrade all three lignocellulosic polymers, providing new evidence for their importance in lignocellulose degradation. Variation in lignin-degrading activity was better explained by microbial community properties, such as catabolic gene content and community structure, than cellulose-degrading activity. SIP significantly improved shotgun metagenome assembly resulting in the recovery of several high-quality draft metagenome-assembled genomes and over 7500 contigs containing unique clusters of carbohydrate-active genes. These results improve understanding of which organisms, conditions and corresponding functional genes contribute to lignocellulose decomposition.

Diversity and temporal shifts of the bacterial community associated with a toxic cyanobacterial bloom: An interplay between microcystin producers and degraders

The biodegradation of microcystins (MCs) by bacteria constitutes an important process in freshwater ecosystems to prevent the accumulation of toxins. However, little is known about the diversity and the seasonal dynamics of the bacterial community composition (BCC) involved in the degradation of MCs in nature. To explore these BCC shifts, high-throughput sequencing was used to analyse the 16S rRNA, mcyE and mlrA genes during a year in a freshwater reservoir with a toxic cyanobacterial bloom episode. The analysis of the mcyE and mlrA genes from water samples revealed the coexistence of different MC-producing and MC-degrading genotypes, respectively. The patchy temporal distribution of the mlrA genotypes (from the families Sphingomonadaceae and Xanthomonadaceae) suggests their dissimilar response to environmental conditions and the influence of other factors besides the MCs that may control their presence and relative abundance. During the maximum toxic cyanobacterial biomass and cell lysis, other bacterial taxa that lack mlr genes increased their relative abundance. Among these bacteria, those with a recognized role in the degradation of xenobiotic and other complex organic compounds (e.g., orders Myxococcales, Ellin6067, Spirobacillales and Cytophagales) were the most representative and suggest their possible involvement in the removal of MCs in the environment.

Draft Genome Sequences of Two Uncultured Armatimonadetes Associated with a Microcystis sp. ( Cyanobacteria ) Isolate

Two genome sequences of the phylum Armatimonadetes, derived from terrestrial environments, have been previously described. Here, two additional Armatimonadetes genome sequences were obtained via single-molecule real-time (SMRT) sequencing of an enrichment culture of the bloom-forming cyanobacterium Microcystis sp. isolated from a eutrophic lake (Brandenburg, Germany). The genomes are most closely affiliated with the class Fimbriimonadales, although they are smaller than the 5.6-Mbp type strain genome.

Long-Term Enrichment of Stress-Tolerant Cellulolytic Soil Populations following Timber Harvesting Evidenced by Multi-Omic Stable Isotope Probing

Soil management is vital for maintaining the productivity of commercial forests, yet the long-term impact of timber harvesting on soil microbial communities remains largely a matter of conjecture. Decomposition of plant biomass, comprised mainly of lignocellulose, has a broad impact on nutrient cycling, microbial activity and physicochemical characteristics of soil. At "Long-term Soil Productivity Study" sites in California dominated by Ponderosa pine, we tested whether clear-cut timber harvesting, accompanied by varying degrees of organic matter (OM) removal, affected the activity and structure of the cellulose-degrading microbial populations 16 years after harvesting. Using a variety of experimental approaches, including stable isotope probing with 13C-labeled cellulose in soil microcosms, we demonstrated that harvesting led to a decrease in net respiration and cellulolytic activity. The decrease in cellulolytic activity was associated with an increased relative abundance of thermophilic, cellulolytic fungi (Chaetomiaceae), coupled with a decreased relative abundance of cellulolytic bacteria, particularly members of Opitutaceae, Caulobacter, and Streptomycetaceae. In general, harvesting led to an increase in stress-tolerant taxa (i.e., also non-cellulolytic taxa), though our results indicated that OM retention mitigated population shifts via buffering against abiotic changes. Stable-isotope probing improved shotgun metagenome assembly by 20-fold and enabled the recovery of 10 metagenome-assembled genomes of cellulolytic bacteria and fungi. Our study demonstrates the putative cellulolytic activity of a number of uncultured taxa and highlights the mineral soil layer as a reservoir of uncharacterized diversity of cellulose-degraders. It also and contributes to a growing body of research showing persistent changes in microbial community structure in the decades following forest harvesting.

Illumina sequencing-based community analysis of bacteria associated with different bryophytes collected from Tibet, China

Background

Previous studies on the bacteria associated with the bryophytes showed that there were abundant bacteria inhabited in/on these hosts. However, the type of bacteria and whether these discriminate between different bryophytes based on a particular factor remains largely unknown.

Results

This study was designed to analyze the biodiversity and community of the bacteria associated with ten liverworts and ten mosses using Illumina-sequencing techniques based on bacterial 16S rRNA gene. A total of 125,762 high quality sequences and 437 OTUs were obtained from twenty bryophytes. Generally, there were no obvious differences between the richness of bacteria associated with liverworts and mosses; however, the diversity was significantly higher in liverworts than in mosses. The taxonomic analyses showed that there were abundant bacteria inhabited with each bryophyte and those primarily detected in all samples were within the phyla Proteobacteria, Actinobacteria, Acidobacteria, Bacteroidetes, Armatimonadetes and Planctomycetes. In addition, bacteria assigned to Chloroflexi, Fibrobacteres, Gemmatimonadetes, Chlamydiae, group of TM6 and WCHB1-60 also appeared in part of the bryophytes. The assigned bacteria included those adapted to aquatic, anaerobic and even extreme drought environments, which is consistent with the bryophyte transition from aquatic to terrestrial conditions. Of them, approximately 10 recognized genera were shared by all the samples in a higher proportion, such as Burkholderia, Novosphingobium, Mucilaginibacter, Sorangium, Frankia, Frondihatitans, Haliangium, Rhizobacter, Granulicella and Hafnia, and 11 unclassified genera were also detected in all samples, which exhibited that large amounts of unclassified bacteria could interact with the bryophytes. The Heatmap and Principle Coordinate Analyses showed that bacteria associated with six mosses displayed a higher community similarity. Notably, the bacteria associated with another four mosses exhibited higher similarity with the ten liverworts.

Conclusions

The result of further analysis of the bacterial community in different bryophytes revealed that the phylogeny of hosts might portray a strong influence on the associated bacterial community and that niche also played important roles when the hosts were phylogenetically more similar. Further studies are needed to confirm the role of phylogeny on bacterial communities and determine the level of influence on predicting which bacteria is associated with the host.

Enrichment of Root Endophytic Bacteria from Populus deltoides and Single-Cell-Genomics Analysis

Bacterial endophytes that colonize Populus trees contribute to nutrient acquisition, prime immunity responses, and directly or indirectly increase both above- and below-ground biomasses. Endophytes are embedded within plant material, so physical separation and isolation are difficult tasks. Application of culture-independent methods, such as metagenome or bacterial transcriptome sequencing, has been limited due to the predominance of DNA from the plant biomass. Here, we describe a modified differential and density gradient centrifugation-based protocol for the separation of endophytic bacteria from Populus roots. This protocol achieved substantial reduction in contaminating plant DNA, allowed enrichment of endophytic bacteria away from the plant material, and enabled single-cell genomics analysis. Four single-cell genomes were selected for whole-genome amplification based on their rarity in the microbiome (potentially uncultured taxa) as well as their inferred abilities to form associations with plants. Bioinformatics analyses, including assembly, contamination removal, and completeness estimation, were performed to obtain single-amplified genomes (SAGs) of organisms from the phyla Armatimonadetes, Verrucomicrobia, and Planctomycetes, which were unrepresented in our previous cultivation efforts. Comparative genomic analysis revealed unique characteristics of each SAG that could facilitate future cultivation efforts for these bacteria.

IMPORTANCE

Plant roots harbor a diverse collection of microbes that live within host tissues. To gain a comprehensive understanding of microbial adaptations to this endophytic lifestyle from strains that cannot be cultivated, it is necessary to separate bacterial cells from the predominance of plant tissue. This study provides a valuable approach for the separation and isolation of endophytic bacteria from plant root tissue. Isolated live bacteria provide material for microbiome sequencing, single-cell genomics, and analyses of genomes of uncultured bacteria to provide genomics information that will facilitate future cultivation attempts.

The Chthonomonas calidirosea Genome Is Highly Conserved across Geographic Locations and Distinct Chemical and Microbial Environments in New Zealand's Taupō Volcanic Zone

Chthonomonas calidirosea T49^T is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. We hypothesized that the C. calidirosea genome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. We tested this hypothesis by sequencing the genomes of four C. calidirosea isolates obtained from four separate geothermal fields in the Taupō Volcanic Zone, New Zealand. For each isolation site, we measured physicochemical attributes and defined the associated microbial community by 16S rRNA gene sequencing. Despite their ecological and geographical isolation, the genome sequences showed low divergence (maximum, 1.17%). Isolate-specific variations included single-nucleotide polymorphisms (SNPs), restriction-modification systems, and mobile elements but few major deletions and no major rearrangements. The 50-fold variation in C. calidirosea relative abundance among the four sites correlated with site environmental characteristics but not with differences in genomic content. Conversely, the carbohydrate utilization profiles of the C. calidirosea isolates corresponded to the inferred isolate phylogenies, which only partially paralleled the geographical relationships among the sample sites. Genomic sequence conservation does not entirely parallel geographic distance, suggesting that stochastic dispersal and localized extinction, which allow for rapid population homogenization with little restriction by geographical barriers, are possible mechanisms of C. calidirosea distribution. This dispersal and extinction mechanism is likely not limited to C. calidirosea but may shape the populations and genomes of many other low-abundance free-living taxa.

IMPORTANCE This study compares the genomic sequence variations and metabolisms of four strains of Chthonomonas calidirosea, a rare thermophilic bacterium from the phylum Armatimonadetes. It additionally compares the microbial communities and chemistry of each of the geographically distinct sites from which the four C. calidirosea strains were isolated. C. calidirosea was previously reported to possess a highly disorganized genome, but it was unclear whether this reflected rapid evolution. Here, we show that each isolation site has a distinct chemistry and microbial community, but despite this, the C. calidirosea genome is highly conserved across all isolation sites. Furthermore, genomic sequence differences only partially paralleled geographic distance, suggesting that C. calidirosea genotypes are not primarily determined by adaptive evolution. Instead, the presence of C. calidirosea may be driven by stochastic dispersal and localized extinction. This ecological mechanism may apply to many other low-abundance taxa.

Stable-Isotope Probing Identifies Uncultured Planctomycetes as Primary Degraders of a Complex Heteropolysaccharide in Soil

The exopolysaccharides (EPSs) produced by some bacteria are potential growth substrates for other bacteria in soil. We used stable-isotope probing (SIP) to identify aerobic soil bacteria that assimilated the cellulose produced by Gluconacetobacter xylinus or the EPS produced by Beijerinckia indica. The latter is a heteropolysaccharide comprised primarily of l-guluronic acid, d-glucose, and d-glycero-d-mannoheptose. (13)C-labeled EPS and (13)C-labeled cellulose were purified from bacterial cultures grown on [(13)C]glucose. Two soils were incubated with these substrates, and bacteria actively assimilating them were identified via pyrosequencing of 16S rRNA genes recovered from (13)C-labeled DNA. Cellulose C was assimilated primarily by soil bacteria closely related (93 to 100% 16S rRNA gene sequence identities) to known cellulose-degrading bacteria. However, B. indica EPS was assimilated primarily by bacteria with low identities (80 to 95%) to known species, particularly by different members of the phylum Planctomycetes. In one incubation, members of the Planctomycetes made up >60% of all reads in the labeled DNA and were only distantly related (<85% identity) to any described species. Although it is impossible with SIP to completely distinguish primary polysaccharide hydrolyzers from bacteria growing on produced oligo- or monosaccharides, the predominance of Planctomycetes suggested that they were primary degraders of EPS. Other bacteria assimilating B. indica EPS included members of the Verrucomicrobia, candidate division OD1, and the Armatimonadetes. The results indicate that some uncultured bacteria in soils may be adapted to using complex heteropolysaccharides for growth and suggest that the use of these substrates may provide a means for culturing new species.

The first complete genome sequence of the class Fimbriimonadia in the phylum Armatimonadetes

In this study, we present the complete genome of Fimbriimonas ginsengisoli Gsoil 348T belonging to the class Fimbriimonadia of the phylum Armatimonadetes, formerly called as candidate phylum OP10. The complete genome contains a single circular chromosome of 5.23 Mb including a 45.5 kb prophage. Of the 4820 open reading frames (ORFs), 3,000 (62.2%) genes could be classified into Clusters of Orthologous Groups (COG) families. With the split of rRNA genes, strain Gsoil 348T had no typical 16S-23S-5S ribosomal RNA operon. In this genome, the GC skew inversion which was usually observed in archaea was found. The predicted gene functions suggest that the organism lacks the ability to synthesize histidine, and the TCA cycle is incomplete. Phylogenetic analyses based on ribosomal proteins indicated that strain Gsoil 348T represents a deeply branching lineage of sufficient divergence with other phyla, but also strongly involved in superphylum Terrabacteria.