Phylogenomic analysis of Candidatus 'Izimaplasma' species: free-living representatives from a Tenericutes clade found in methane seeps

Effects of Fructus Aurantii Extract on Growth Performance, Nutrient Apparent Digestibility, Serum Parameters, and Fecal Microbiota in Finishing Pigs

This study investigated the effects of Fructus Aurantii extract (FAE) on growth performance, nutrient apparent digestibility, serum parameters, fecal microbial composition, and short-chain fatty acids (SCFAs) in finishing pigs. In total, 75 Duroc × Landrace × Yorkshire pigs (equally divided by sex), with an initial body weight of 79.49 ± 4.27 kg, were randomly assigned to three treatment groups. The pigs were fed either a basic diet (CON) or a basal diet supplemented with 500 mg/kg of FAE (FAE500) and 1000 mg/kg of FAE (FAE1000). The FAE1000 group exhibited a significantly higher final body weight (FBW) (p < 0.05), and the average daily feed intake (ADFI) showed an increasing tendency in the FAE500 and FAE1000 groups (p = 0.056) compared to the CON group. Additionally, the inclusion of FAE resulted in the significantly higher apparent digestibility of crude ash (Ash), gross energy (GE), and crude protein (CP) (p < 0.05), with a tendency to the increased digestibility of dry matter (DM) (p = 0.053). Dietary FAE supplementation led to elevated serum levels of reduced glutathione (GSH) and decreased levels of serum L-lactic dehydrogenase (LDH), along with a tendency to increase serum glucose (GLU) levels (p = 0.084). The FAE500 group demonstrated higher serum concentrations of motilin (MTL) and gastrin (GAS) (p < 0.05), and a tendency for reduced serum glucagon-like peptide-1 (GLP-1) level (p = 0.055) compared to the CON group. Furthermore, alpha diversity analysis revealed that the FAE500 group significantly increased the Chao 1 and Observed_species indexes (p < 0.05). Similarly, beta diversity analysis indicated that FAE feeding altered the fecal microbial structure (p = 0.083). Notably, compared with the control group, CF231, Pediococcus, and Mogibacterium displayed higher relative abundance in the feces of the FAE500 group, whereas Tenericutes showed a reduction in relative abundance (p < 0.05). Additionally, the relative abundance of Tenericute was negatively correlated with the digestibility of DM, GE, Ash, and CP (p < 0.05). Serum MTL and GAS levels correlated positively with the Coprococcus, Dorea, Pediococcus, and Mogibacterium relative abundances (p < 0.05). Collectively, dietary FAE supplementation could enhance growth performance by boosting beneficial bacteria in feces, stimulating gastrointestinal hormone secretion, and improving nutrient digestibility.

Organic matter degradation in the deep, sulfidic waters of the Black Sea: insights into the ecophysiology of novel anaerobic bacteria

BACKGROUND

Recent studies have reported the identity and functions of key anaerobes involved in the degradation of organic matter (OM) in deep (> 1000 m) sulfidic marine habitats. However, due to the lack of available isolates, detailed investigation of their physiology has been precluded. In this study, we cultivated and characterized the ecophysiology of a wide range of novel anaerobes potentially involved in OM degradation in deep (2000 m depth) sulfidic waters of the Black Sea.

RESULTS

We have successfully cultivated a diverse group of novel anaerobes belonging to various phyla, including Fusobacteriota (strain S5), Bacillota (strains A1T and A2), Spirochaetota (strains M1T, M2, and S2), Bacteroidota (strains B1T, B2, S6, L6, SYP, and M2P), Cloacimonadota (Cloa-SY6), Planctomycetota (Plnct-SY6), Mycoplasmatota (Izemo-BS), Chloroflexota (Chflx-SY6), and Desulfobacterota (strains S3T and S3-i). These microorganisms were able to grow at an elevated hydrostatic pressure of up to 50 MPa. Moreover, this study revealed that different anaerobes were specialized in degrading specific types of OM. Strains affiliated with the phyla Fusobacteriota, Bacillota, Planctomycetota, and Mycoplasmatota were found to be specialized in the degradation of cellulose, cellobiose, chitin, and DNA, respectively, while strains affiliated with Spirochaetota, Bacteroidota, Cloacimonadota, and Chloroflexota preferred to ferment less complex forms of OM. We also identified members of the phylum Desulfobacterota as terminal oxidizers, potentially involved in the consumption of hydrogen produced during fermentation. These results were supported by the identification of genes in the (meta)genomes of the cultivated microbial taxa which encode proteins of specific metabolic pathways. Additionally, we analyzed the composition of membrane lipids of selected taxa, which could be critical for their survival in the harsh environment of the deep sulfidic waters and could potentially be used as biosignatures for these strains in the sulfidic waters of the Black Sea.

CONCLUSIONS

This is the first report that demonstrates the cultivation and ecophysiology of such a diverse group of microorganisms from any sulfidic marine habitat. Collectively, this study provides a step forward in our understanding of the microbes thriving in the extreme conditions of the deep sulfidic waters of the Black Sea. Video Abstract.

Genetic evidence on the causality between gut microbiota and various asthma phenotypes: a two-sample Mendelian randomization study

Introduction

Asthma is a multifarious disease that manifests in various phenotypes. Among the various factors that contribute to the development of asthma, the gut microbiota has recently emerged as a compelling area of investigation. This study aims to investigate the causal relationships between gut microbiota and distinct asthma phenotypes.

Methods

The genome-wide association study (GWAS) summary statistics for 211 gut microbial taxa were used as study exposure. Five traits pertaining to various asthma phenotypes (asthma, allergic asthma, childhood asthma, suggestive for eosinophilic asthma and obesity-related asthma) were included as study outcome. We conducted Mendelian randomization (MR) analysis and sensitivity analysis for each bacterial taxa and asthma phenotypes.

Result

We discovered a total of 58 associations that exhibited evidence of causality. Out of these, 4 associations remained significant even after applying multiple correction. An increased risk of asthma was causally associated with higher abundance of genus Holdemanella (OR = 1.11; CI: 1.05-1.17; p = 0.027), genus Oxalobacter (OR = 1.09; CI: 1.04-1.15; p = 0.025) and genus Butyricimonas (OR = 1.14; CI: 1.06-1.22; p = 0.027). Order NB1n was causally linked with an increased risk of obesity-related asthma (OR = 1.17; CI: 1.07-1.29; p = 0.015). There was limited overlap among the taxa that exhibited potential causal relationships with distinct asthma phenotypes.

Conclusion

Our research has provided genetic evidence that establishes multiple causal relationships between the gut microbiota and distinct asthma phenotypes, supporting the role of the gut microbiota in various asthma phenotypes. It is possible that different taxa play a role in the development of distinct asthma phenotypes. The causal relationships identified in this study require further investigation.

Scaling of Protein Function across the Tree of Life

Scaling laws are a powerful way to compare genomes because they put all organisms onto a single curve and reveal nontrivial generalities as genomes change in size. The abundance of functional categories across genomes has previously been found to show power law scaling with respect to the total number of functional categories, suggesting that universal constraints shape genomic category abundance. Here, we look across the tree of life to understand how genome evolution may be related to functional scaling. We revisit previous observations of functional genome scaling with an expanded taxonomy by analyzing 3,726 bacterial, 220 archaeal, and 79 unicellular eukaryotic genomes. We find that for some functional classes, scaling is best described by multiple exponents, revealing previously unobserved shifts in scaling as genome-encoded protein annotations increase or decrease. Furthermore, we find that scaling varies between phyletic groups at both the domain and phyla levels and is less universal than previously thought. This variability in functional scaling is not related to taxonomic phylogeny resolved at the phyla level, suggesting that differences in cell plan or physiology outweigh broad patterns of taxonomic evolution. Since genomes are maintained and replicated by the functional proteins encoded by them, these results point to functional degeneracy between taxonomic groups and unique evolutionary trajectories toward these. We also find that individual phyla frequently span scaling exponents of functional classes, revealing that individual clades can move across scaling exponents. Together, our results reveal unique shifts in functions across the tree of life and highlight that as genomes grow or shrink, proteins of various functions may be added or lost.

Natural and anthropogenic carbon input affect microbial activity in salt marsh sediment

Salt marshes are dynamic, highly productive ecosystems positioned at the interface between terrestrial and marine systems. They are exposed to large quantities of both natural and anthropogenic carbon input, and their diverse sediment-hosted microbial communities play key roles in carbon cycling and remineralization. To better understand the effects of natural and anthropogenic carbon on sediment microbial ecology, several sediment cores were collected from Little Sippewissett Salt Marsh (LSSM) on Cape Cod, MA, USA and incubated with either Spartina alterniflora cordgrass or diesel fuel. Resulting shifts in microbial diversity and activity were assessed via bioorthogonal non-canonical amino acid tagging (BONCAT) combined with fluorescence-activated cell sorting (FACS) and 16S rRNA gene amplicon sequencing. Both Spartina and diesel amendments resulted in initial decreases of microbial diversity as well as clear, community-wide shifts in metabolic activity. Multi-stage degradative frameworks shaped by fermentation were inferred based on anabolically active lineages. In particular, the metabolically versatile Marinifilaceae were prominent under both treatments, as were the sulfate-reducing Desulfovibrionaceae, which may be attributable to their ability to utilize diverse forms of carbon under nutrient limited conditions. By identifying lineages most directly involved in the early stages of carbon processing, we offer potential targets for indicator species to assess ecosystem health and highlight key players for selective promotion of bioremediation or carbon sequestration pathways.

Mechanisms of nucleic acid degradation and high hydrostatic pressure tolerance of a novel deep-sea wall-less bacterium

Wall-less bacteria are broadly distributed in diverse habitats. They evolved from a common ancestor within the Firmicutes phylum through reductive evolution. Here, we report the cultivation, characterization, and polyphasic taxonomic analysis of the novel free-living wall-less bacterium, Hujiaoplasma nucleasis zrk29. We demonstrated that strain zrk29 had a strong ability to degrade DNA and RNA both under laboratory conditions and in the deep sea. We found that nucleic acids induced strain zrk29 to release chronic bacteriophages which supported strain zrk29 and other marine bacteria to metabolize nucleic acids without lysing host cells. We also showed that strain zrk29 tolerated high hydrostatic pressure via two pathways: (i) by transporting cations into its cells to increase intracellular osmotic pressure and (ii) by adjusting the unsaturated fatty acid chain content in its cell membrane phospholipids to increase cell membrane fluidity. This study extends our understanding of free-living wall-less bacteria and provides a useful model to explore the unique adaptation mechanisms of deep-sea microbes. IMPORTANCE The unique physiology and survival strategies of the Tenericutes bacterium-a typical wall-less bacterium-have fascinated scientists and the public, especially in extreme deep-sea environments where there is high hydrostatic pressure (HHP) and limited availability of nutrients. Here, we have isolated a novel free-living Tenericutes strain from deep-sea sediment and have found that it metabolizes nucleic acids with the support of chronic bacteriophages. This Tenericutes strain tolerates HHP stress by increasing intracellular osmotic pressure and the unsaturated fatty acid chain content of phospholipids in its cell membrane. Our results provide insights into the unique physiology of deep-sea free-living Tenericutes bacteria and highlight the significant role that chronic bacteriophages play in assisting wall-less bacteria to adapt to harsh conditions.

The associations between gut microbiota and chronic respiratory diseases: a Mendelian randomization study

Introduction

Growing evidence indicates that variations in the composition of the gut microbiota are linked to the onset and progression of chronic respiratory diseases (CRDs), albeit the causal relationship between the two remains unclear.

Methods

We conducted a comprehensive two-sample Mendelian randomization (MR) analysis to investigate the relationship between gut microbiota and five main CRDs, including chronic obstructive pulmonary disease (COPD), asthma, idiopathic pulmonary fibrosis (IPF), sarcoidosis, and pneumoconiosis. For MR analysis, the inverse variance weighted (IVW) method was utilized as the primary method. The MR-Egger, weighted median, and MR-PRESSO statistical methods were used as a supplement. To detect heterogeneity and pleiotropy, the Cochrane and Rucker Q test, MR-Egger intercept test, and MR-PRESSO global test were then implemented. The leave-one-out strategy was also applied to assess the consistency of the MR results.

Results

Based on substantial genetic data obtained from genome-wide association studies (GWAS) comprising 3,504,473 European participants, our study offers evidence that several gut microbial taxa, including 14 probable microbial taxa (specifically, 5, 3, 2, 3 and 1 for COPD, asthma, IPF, sarcoidosis, and pneumoconiosis, respectively) and 33 possible microbial taxa (specifically, 6, 7, 8, 7 and 5 for COPD, asthma, IPF, sarcoidosis, and pneumoconiosis, respectively) play significant roles in the formation of CRDs.

Discussion

This work implies causal relationships between the gut microbiota and CRDs, thereby shedding new light on the gut microbiota-mediated prevention of CRDs.

Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis

At particular stages during their life cycles, fungi use multiple strategies to form specialized structures to survive unfavorable environmental conditions. These strategies encompass sporulation, as well as cell-wall melanization, multicellular tissue formation or even dimorphism. The resulting structures are not only used to disperse to other environments, but also to survive long periods of time awaiting favorable growth conditions. As a result, these specialized fungal structures are part of the microbial seed bank, which is known to influence the microbial community composition and contribute to the maintenance of diversity. Despite the importance of the microbial seed bank in the environment, methods to study the diversity of fungal structures with improved resistance only target spores dispersing in the air, omitting the high diversity of these structures in terms of morphology and environmental distribution. In this study, we applied a separation method based on cell lysis to enrich lysis-resistant fungal structures (for instance, spores, sclerotia, melanized yeast) to obtain a proxy of the composition of the fungal seed bank. This approach was first evaluated in-vitro in selected species. The results obtained showed that DNA from fungal spores and from yeast was only obtained after the application of the enrichment method, while mycelium was always lysed. After validation, we compared the diversity of the total and lysis-resistant fractions in the polyextreme environment of the Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano. Environmental samples were collected from the salt flat and from microbial mats in small surrounding ponds. Both the lake sediments and microbial mats were dominated by Ascomycota and Basidiomycota, however, the diversity and composition of each environment differed at lower taxonomic ranks. Members of the phylum Chytridiomycota were enriched in the lysis-resistant fraction, while members of the phylum Rozellomycota were never detected in this fraction. Moreover, we show that the community composition of the lysis-resistant fraction reflects the diversity of life cycles and survival strategies developed by fungi in the environment. To the best of our knowledge this is the first time that the fungal diversity is explored in the Salar de Huasco. In addition, the method presented here provides a simple and culture independent approach to assess the diversity of fungal lysis-resistant cells in the environment.

Corinthian Currants Supplementation Restores Serum Polar Phenolic Compounds, Reduces IL-1beta, and Exerts Beneficial Effects on Gut Microbiota in the Streptozotocin-Induced Type-1 Diabetic Rat

The present study aimed at investigating the possible benefits of a dietary intervention with Corinthian currants, a rich source of phenolic compounds, on type 1 diabetes (T1D) using the animal model of the streptozotocin-(STZ)-induced diabetic rat. Male Wistar rats were randomly assigned into four groups: control animals, which received a control diet (CD) or a diet supplemented with 10% w/w Corinthian currants (CCD), and diabetic animals, which received a control diet (DCD) or a currant diet (DCCD) for 4 weeks. Plasma biochemical parameters, insulin, polar phenolic compounds, and inflammatory factors were determined. Microbiota populations in tissue and intestinal fluid of the caecum, as well as fecal microbiota populations and short-chain fatty acids (SCFAs), were measured. Fecal microbiota was further analyzed by 16S rRNA sequencing. The results of the study showed that a Corinthian currant-supplemented diet restored serum polar phenolic compounds and decreased interleukin-1b (IL-1b) (p < 0.05) both in control and diabetic animals. Increased caecal lactobacilli counts (p < 0.05) and maintenance of enterococci levels within normal range were observed in the intestinal fluid of the DCCD group (p < 0.05 compared to DCD). Higher acetic acid levels were detected in the feces of diabetic rats that received the currant diet compared to the animals that received the control diet (p < 0.05). Corinthian currant could serve as a beneficial dietary component in the condition of T1D based on the results coming from the animal model of the STZ-induced T1D rat.

Dietary ellagic acid supplementation attenuates intestinal damage and oxidative stress by regulating gut microbiota in weanling piglets

Intestinal oxidative stress triggers gut microbiota dysbiosis, which is involved in the etiology of post-weaning diarrhea and enteric infections. Ellagic acid (EA) can potentially serve as an antioxidant supplement to facilitate weaning transition by improving intestinal oxidative stress and gut microbiota dysbiosis. Therefore, we aimed to investigate the effects of dietary EA supplementation on the attenuation of intestinal damage, oxidative stress, and dysbiosis of gut microbiota in weanling piglets. A total of 126 piglets were randomly assigned into 3 groups and treated with a basal diet and 2 mL saline orally (Ctrl group), or the basal diet supplemented with 0.1% EA and 2 mL saline orally (EA group), or the basal diet and 2 mL fecal microbiota suspension from the EA group orally (FEA group), respectively, for 14 d. Compared with the Ctrl group, EA group improved growth performance by increasing average daily feed intake and average daily weight gain (P < 0.05) and decreasing fecal scores (P < 0.05). EA group also alleviated intestinal damage by increasing the tight junction protein occludin (P < 0.05), villus height, and villus height-to-crypt depth ratio (P < 0.05), while decreasing intestinal epithelial apoptosis (P < 0.05). Additionally, EA group enhanced the jejunum antioxidant capacity by increasing the total antioxidant capacity (P < 0.01), catalase (P < 0.05), and glutathione/oxidized glutathione (P < 0.05), but decreased the oxidative metabolite malondialdehyde (P < 0.05) compared to the Ctrl group. Compared with the Ctrl group, EA and FEA groups increased alpha diversity (P < 0.05), enriched beneficial bacteria (Ruminococcaceae and Clostridium ramosum), and increased metabolites short-chain fatty acids (P < 0.05). Correspondingly, FEA group gained effects comparable to those of EA group on growth performance, intestinal damage, and intestinal antioxidant capacity. In addition, the relative abundance of bacteria shifted in EA and FEA groups was significantly related to the examined indices (P < 0.05). Overall, dietary EA supplementation could improve growth performance and attenuate intestinal damage and oxidative stress by regulating the gut microbiota in weanling piglets.

Changes in the gut microbiota of forest musk deer (Moschus berezovskii) during ex situ conservation

Ex situ conservation is an important technique for protecting rare and endangered wildlife, and maintaining stable individual health is crucial to its success. Gut microbiota composition is a critical indicator of animal health and should therefore be closely monitored during ex situ conservation to track impacts on animal health. Forest musk deer (Moschus berezovskii) were historically distributed in Hebei Province, China, however, they are now extinct in the region. Thus, ex situ conservation efforts were conducted in 2016 whereby approximately 50 individuals were artificially migrated from Weinan, Shaanxi to Huailai, Hebei. To monitor gut health of these migrated individuals, we used 16S rRNA high-throughput sequencing technology to examine the microbiota differences between Huailai juvenile and Weinan juvenile groups, and between Huailai adult and Weinan adult groups. Alpha diversity analysis indicated that the richness of microbiota significantly decreased after migration to the Huailai area, and the beta diversity results also showed significant dissimilarity in gut microbial communities, demonstrating the distinct microbial structure differences in the forest musk deer population from the two areas, for both juvenile and adult groups, respectively. In addition, PICRUSt functional profile prediction indicated that the functions of gut digestion and absorption, and degradation of toxic substances were significantly weakened after ex situ conservation. Differences in diet composition between the individuals of the two sites were also observed and the impact of food on gut microbiota compositions within forest musk deer during ex situ conservation was investigated. This study provides a theoretical basis for developing ex situ conservation measures, especially for the protection of forest musk deer.

Host species and habitats shape the bacterial community of gut microbiota of three non-human primates: Siamangs, white-handed gibbons, and Bornean orangutans

The gut microbiome is essential for a host to digest food, maintain health, and adapt to environments. Bacterial communities of gut microbiota are influenced by diverse factors including host physiology and the environment. Many non-human primates (NHPs), which are physiologically close to humans, are in danger of extinction. In this study, the community structure of the gut microbiota in three NHPs: siamangs (Symphalangus syndactylus, Ss), Bornean orangutans (Pongo pygmaeus, Pp), and white-handed gibbons (Hylobates lar, Hl)—housed at the largest Zoo in Taiwan were analyzed. Pp and Ss were housed in the Asian tropical rainforest area, while Hl was housed in two separate areas, the Asian tropical rainforest area and the conservation area. Bacterial community diversity of Ss, indicated by the Shannon index, was significantly higher compared with that of Hl and Pp, while the richness (Chao 1) and observed operational taxonomic units (OTUs) were similar across the three species of NHPs. Host species was the dominant factor shaping the gut microbial community structure. Beta-diversity analysis including non-metric multidimensional scaling (NMDS) and unweighted pair group method with arithmetic mean (UPGMA) suggested gut bacterial communities of Hl housed in the conservation area were closely related to each other, while the bacterial communities of Hl in the rainforest area were dispersedly positioned. Further analysis revealed significantly higher abundances of Lactobacillus fermentum, L. murinus, and an unclassified species of Lactobacillus, and a lower abundance of Escherichia-Shigella in Hl from the conservation area relative to the rainforest area. The ratio of Lactobacillus to Escherichia-Shigella was 489.35 and 0.013 in Hl inhabiting the conservation and rainforest areas, respectively. High abundances of Lactobacillus and Bifidobacterium and a high ratio of Lactobacillus to Escherichia-Shigella were also observed in one siamang with notable longevity of 53 years. Data from the study reveal that host species acted as the fundamental driving factor in modulating the community structure of gut microbiota, but that habitats also acted as key determinants within species. The presence and high abundance of probiotics, such as Bifidobacterium and Lactobacillus, provide potential indicators for future diet and habitat optimization for NHPs, especially in zoological settings.

Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily

Hydrothermal vents have been key to our understanding of the limits of life, and the metabolic and phylogenetic diversity of thermophilic organisms. Here we used environmental metagenomics combined with analysis of physicochemical data and 16S rRNA gene amplicons to characterize the sediment-hosted microorganisms at the recently discovered Auka vents in the Gulf of California. We recovered 325 metagenome assembled genomes (MAGs) representing 54 phyla, over 30% of those currently known, showing the microbial community in Auka hydrothermal sediments is highly diverse. 16S rRNA gene amplicon screening of 224 sediment samples across the vent field indicates that the MAGs retrieved from a single site are representative of the microbial community in the vent field sediments. Metabolic reconstruction of a vent-specific, deeply branching clade within the Desulfobacterota suggests these organisms metabolize sulfur using novel octaheme cytochrome-c proteins related to hydroxylamine oxidoreductase. Community-wide comparison between Auka MAGs and MAGs from Guaymas Basin revealed a remarkable 20% species-level overlap, suggestive of long-distance species transfer over 400 km and subsequent sediment colonization. Optimal growth temperature prediction on the Auka MAGs, and thousands of reference genomes, shows that thermophily is a trait that has evolved frequently. Taken together, our Auka vent field results offer new perspectives on our understanding of hydrothermal vent microbiology.

The treatment of Qibai Pingfei Capsule on chronic obstructive pulmonary disease may be mediated by Th17/Treg balance and gut-lung axis microbiota

BACKGROUND

Chronic obstructive pulmonary disease (COPD), a prevalent, progressive respiratory disease, has become the third leading cause of death globally. Increasing evidence suggests that intestinal and pulmonary microbiota dysbiosis is associated with COPD. Researchers have shown that T helper (Th) 17/regulatory T (Treg) imbalance is involved in COPD. Qibai Pingfei Capsule (QBPF) is a traditional Chinese medicine used to treat COPD clinically in China. However, the effects of QBPF intervention on the Th17/Treg balance and microbiota in the gut and lung are still poorly understood.

METHODS

This study divided the rats into three groups (n = 8): control, model, and QBPF group. After establishing the model of COPD for four weeks and administering of QBPF for two weeks, Th17 cells, Treg cells, their associated cytokines, transcription factors, and intestinal and pulmonary microbiota of rats were analyzed. Furthermore, the correlations between intestinal and pulmonary microbiota and between bacterial genera and pulmonary function and immune function were measured.

RESULTS

The results revealed that QBPF could improve pulmonary function and contribute to the new balance of Th17/Treg in COPD rats. Meanwhile, QBPF treatment could regulate the composition of intestinal and pulmonary microbiota and improve community structure in COPD rats, suppressing the relative abundance of Coprococcus_2, Prevotella_9, and Blautia in the gut and Mycoplasma in the lung, but accumulating the relative abundance of Prevotellaceae_UCG_003 in the gut and Rikenellaceae_RC9_gut_group in the lung. Additionally, gut-lung axis was confirmed by the significant correlations between the intestinal and pulmonary microbiota. Functional analysis of microbiota showed amino acid metabolism was altered in COPD rats in the gut and lung. Spearman correlation analysis further enriched the relationship between the microbiota in the gut and lung and pulmonary function and immune function in COPD model rats.

CONCLUSIONS

Our study indicated that the therapeutic effects of QBPF may be achieved by maintaining the immune cell balance and regulating the gut-lung axis microbiota, providing references to explore the potential biomarkers of COPD and the possible mechanism of QBPF to treat COPD.

Diversity of Lysis-Resistant Bacteria and Archaea in the Polyextreme Environment of Salar de Huasco

The production of specialized resting cells is a remarkable strategy developed by several organisms to survive unfavorable environmental conditions. Spores are specialized resting cells that are characterized by low to absent metabolic activity and higher resistance. Spore-like cells are known from multiple groups of bacteria, which can form spores under suboptimal growth conditions (e.g., starvation). In contrast, little is known about the production of specialized resting cells in archaea. In this study, we applied a culture-independent method that uses physical and chemical lysis, to assess the diversity of lysis-resistant bacteria and archaea and compare it to the overall prokaryotic diversity (direct DNA extraction). The diversity of lysis-resistant cells was studied in the polyextreme environment of the Salar de Huasco. The Salar de Huasco is a high-altitude athalassohaline wetland in the Chilean Altiplano. Previous studies have shown a high diversity of bacteria and archaea in the Salar de Huasco, but the diversity of lysis-resistant microorganisms has never been investigated. The underlying hypothesis was that the combination of extreme abiotic conditions might favor the production of specialized resting cells. Samples were collected from sediment cores along a saline gradient and microbial mats were collected in small surrounding ponds. A significantly different diversity and composition were found in the sediment cores or microbial mats. Furthermore, our results show a high diversity of lysis-resistant cells not only in bacteria but also in archaea. The bacterial lysis-resistant fraction was distinct in comparison to the overall community. Also, the ability to survive the lysis-resistant treatment was restricted to a few groups, including known spore-forming phyla such as Firmicutes and Actinobacteria. In contrast to bacteria, lysis resistance was widely spread in archaea, hinting at a generalized resistance to lysis, which is at least comparable to the resistance of dormant cells in bacteria. The enrichment of Natrinema and Halarchaeum in the lysis-resistant fraction could hint at the production of cyst-like cells or other resistant cells. These results can guide future studies aiming to isolate and broaden the characterization of lysis-resistant archaea.

Comparative analysis of microbial communities from different full-scale haloalkaline biodesulfurization systems

Abstract

In biodesulfurization (BD) at haloalkaline and dO₂-limited conditions, sulfide-oxidizing bacteria (SOB) effectively convert sulfide into elemental sulfur that can be used in agriculture as a fertilizer and fungicide. Here we show which bacteria are present in this biotechnological process. 16S rRNA gene amplicon sequencing of biomass from ten reactors sampled in 2018 indicated the presence of 444 bacterial Amplicon Sequence Variants (ASVs). A core microbiome represented by 30 ASVs was found in all ten reactors, with Thioalkalivibrio sulfidiphilus as the most dominant species. The majority of these ASVs are phylogenetically related to bacteria previously identified in haloalkaline BD processes and in natural haloalkaline ecosystems. The source and composition of the feed gas had a great impact on the microbial community composition followed by alkalinity, sulfate, and thiosulfate concentrations. The halophilic SOB of the genus Guyparkeria (formerly known as Halothiobacillus) and heterotrophic SOB of the genus Halomonas were identified as potential indicator organisms of sulfate and thiosulfate accumulation in the BD process.

Key points

• Biodesulfurization (BD) reactors share a core microbiome

• The source and composition of the feed gas affects the microbial composition in the BD reactors

• Guyparkeria and Halomonas indicate high concentrations of sulfate and thiosulfate in the BD process

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-11771-y.

Experimental Periodontitis Deteriorated Atherosclerosis Associated With Trimethylamine N-Oxide Metabolism in Mice

Background

Periodontitis is considered a risk factor for atherosclerosis, but the mechanism is not clear. It was reported that oral administration of Porphyromonas gingivalis altered the gut microbiota in mice. Gut dysbiosis and the intestinal metabolite trimethylamine N-oxide (TMAO) were verified to be associated with atherosclerosis. Therefore, the possible TMAO-related mechanism between periodontitis and atherosclerosis needs to be explored.

Methods

Experimental periodontitis was established by oral administration of P. gingivalis for 2 months in ApoE^−/− mice. Mouse hemi-mandibles were scanned using Micro-CT. Quantification of TMAO was performed using liquid chromatography–tandem mass spectrometry. Mouse feces were collected and the bacterial DNA was extracted, then the gut microbiota was analyzed using 16S rRNA genes. Atherosclerotic lesion areas were quantified. Livers, small intestines, and large intestines were analyzed for gene expression.

Results

Aggravated atherosclerosis plaques were found in experimental periodontitis mice. Plasma TMAO, a pathogenic factor of atherosclerosis, was initially found to be increased in periodontitis mice. Changes in the composition and abundance of the intestinal microflora of periodontitis mice were found. Flavin monooxygenase 3 (FMO3), the catalyzing enzyme of TMAO in the liver, was significantly increased, accompanied by an increase of IL-6 in liver, the abnormal intestinal integrity and enhanced plasma LPS. The IL-6 and LPS were verified to be able to increase FMO3 in HepG2 cells.

Conclusion

Our research discovered that experimental periodontitis in ApoE^−/− mice induced gut dysbiosis and an increase in TMAO. These results suggest a possible mechanism by which periodontitis may accelerate atherosclerosis by influencing the intestinal microbes and the metabolism, which were triggered by inflammation of the liver and intestine.

Effects of microplastics accumulation on performance of membrane bioreactor for wastewater treatment

The effective interception of membrane leads to the accumulation of microplastics (MPs) in membrane bioreactor (MBR) process for long-term operation. However, the influence of MPs accumulation on the performance of MBR hasn't been well understood. In this study, the accumulation of polypropylene microplastics (PP-MPs) in two MBRs run for 3 yr with or without discharging sludge was simulated by operating the lab-scale MBRs for 84 days. The variations of pollutant removal, membrane fouling, composition of soluble microbial product (SMP) and extracellular polymeric substance (EPS), and microbial community of MBRs were systematically investigated. The results show that the removal efficiency of COD and NH₄⁺-N was not depressed by PP-MPs accumulation. However, the presence of PP-MPs in the range of 0.14-0.30 g/L could inhibit the growth of microorganisms, enhance the secretion of SMP and EPS, and reduce the microbial richness and diversity. In the contrary, the high concentration of PP-MPs (2.34-5.00 g/L) exhibited the opposite effects and mitigated membrane fouling, suggesting the important role of MPs concentration. It was also found that the exposure to high concentration of PP-MPs enhanced relative abundance of Clostridia, and inhibited the growth of Proteobacteria. The findings of this study provide a foresight to understand the effects of MPs accumulation on the performance of MBRs.

Mariniplasma anaerobium gen. nov., sp. nov., a novel anaerobic marine mollicute, and proposal of three novel genera to reclassify members of Acholeplasma clusters II-IV

A novel strictly anaerobic chemoorganotrophic bacterium, designated Mahy22^T, was isolated from sulfidic bottom water of a shallow brackish meromictic lake in Japan. Cells of the strain were Gram-stain-negative, non-motile and coccoid in shape with diameters of about 600-800 nm. The temperature range for growth was 15-37 °C, with optimum growth at 30-32 °C. The pH range for growth was pH 6.2-8.9, with optimum growth at pH 7.2-7.4. The strain grew with NaCl concentrations of 5% or below (optimum, 2-3%). Growth of the strain was enhanced by the addition of thiosulfate. The major cellular fatty acids were C_16:0 and anteiso-C_15:0. Respiratory quinones were not detected. The complete genome sequence of strain Mahy22^T possessed a 1 885 846 bp circular chromosome and a 12 782 bp circular genetic element. The G+C content of the genome sequence was 30.1 mol%. Phylogenetic analysis based on the 16S rRNA gene revealed that the novel strain belonged to the family Acholeplasmataceae, class Mollicutes. The closest relative of strain Mahy22^T with a validly published name was Acholeplasma palmae J233^T with a 16S rRNA gene sequence similarity of 90.5%. Based on the results of polyphasic analysis, the name Mariniplasma anaerobium gen. nov., sp. nov. is proposed to accommodate strain Mahy22^T, along with reclassification of some Acholeplasma species into Alteracholeplasma gen. nov., Haploplasma gen. nov. and Paracholeplasma gen. nov.

Endocannabinoid Anandamide Attenuates Acute Respiratory Distress Syndrome through Modulation of Microbiome in the Gut-Lung Axis

Acute respiratory distress syndrome (ARDS) is a serious lung condition characterized by severe hypoxemia leading to limitations of oxygen needed for lung function. In this study, we investigated the effect of anandamide (AEA), an endogenous cannabinoid, on Staphylococcal enterotoxin B (SEB)-mediated ARDS in female mice. Single-cell RNA sequencing data showed that the lung epithelial cells from AEA-treated mice showed increased levels of antimicrobial peptides (AMPs) and tight junction proteins. MiSeq sequencing data on 16S RNA and LEfSe analysis demonstrated that SEB caused significant alterations in the microbiota, with increases in pathogenic bacteria in both the lungs and the gut, while treatment with AEA reversed this effect and induced beneficial bacteria. AEA treatment suppressed inflammation both in the lungs as well as gut-associated mesenteric lymph nodes (MLNs). AEA triggered several bacterial species that produced increased levels of short-chain fatty acids (SCFAs), including butyrate. Furthermore, administration of butyrate alone could attenuate SEB-mediated ARDS. Taken together, our data indicate that AEA treatment attenuates SEB-mediated ARDS by suppressing inflammation and preventing dysbiosis, both in the lungs and the gut, through the induction of AMPs, tight junction proteins, and SCFAs that stabilize the gut-lung microbial axis driving immune homeostasis.

Genomic insights into diverse bacterial taxa that degrade extracellular DNA in marine sediments

Extracellular DNA is a major macromolecule in global element cycles, and is a particularly crucial phosphorus, nitrogen and carbon source for microorganisms in the seafloor. Nevertheless, the identities, ecophysiology and genetic features of DNA-foraging microorganisms in marine sediments are largely unknown. Here, we combined microcosm experiments, DNA stable isotope probing (SIP), single-cell SIP using nano-scale secondary isotope mass spectrometry (NanoSIMS) and genome-centric metagenomics to study microbial catabolism of DNA and its subcomponents in marine sediments. 13C-DNA added to sediment microcosms was largely degraded within 10 d and mineralized to 13CO2. SIP probing of DNA revealed diverse 'Candidatus Izemoplasma', Lutibacter, Shewanella and Fusibacteraceae incorporated DNA-derived 13C-carbon. NanoSIMS confirmed incorporation of 13C into individual bacterial cells of Fusibacteraceae sorted from microcosms. Genomes of the 13C-labelled taxa all encoded enzymatic repertoires for catabolism of DNA or subcomponents of DNA. Comparative genomics indicated that diverse 'Candidatus Izemoplasmatales' (former Tenericutes) are exceptional because they encode multiple (up to five) predicted extracellular nucleases and are probably specialized DNA-degraders. Analyses of additional sediment metagenomes revealed extracellular nuclease genes are prevalent among Bacteroidota at diverse sites. Together, our results reveal the identities and functional properties of microorganisms that may contribute to the key ecosystem function of degrading and recycling DNA in the seabed.

Builders, tenants, and squatters: the origins of genetic material in modern stromatolites

Micro-organisms have long been implicated in the construction of stromatolites. Yet, establishing a microbial role in modern stromatolite growth via molecular analysis is not always straightforward because DNA in stromatolites can have multiple origins. For example, the genomic material could represent the microbes responsible for the construction of the stromatolite (i.e., "builders"), microbes that inhabited the structure after it was built (i.e., "tenants"), or microbes/organic matter that were passively incorporated after construction from the water column or later diagenetic fluids (i.e., "squatters"). Disentangling the role of micro-organisms in stromatolite construction, already difficult in modern systems, becomes more difficult as organic signatures degrade, and their context is obscured. To evaluate our ability to accurately decipher the role of micro-organisms in stromatolite formation in geologically recent settings, 16/18S SSU rRNA gene sequences were analyzed from three systems where the context of growth was well understood: (a) an actively growing stromatolite from a silicic hot spring in Yellowstone National Park, Wyoming, where the construction of the structure is controlled by cyanobacteria; (b) a mixed carbonate and silica precipitate from Little Hot Creek, a hot spring in the Long Valley Caldera of California that has both abiogenic and biogenic components to accretion; and (c) a near-modern lacustrine carbonate stromatolite from Walker Lake, Nevada that is likely abiogenic. In all cases, the largest percentage of recovered DNA sequences, especially when focused on the deeper portions of the structures, belonged to either the tenant or squatter communities, not the actual builders. Once removed from their environmental context, correct interpretation of biology's role in stromatolite morphogenesis was difficult. Because high-throughput genomic analysis may easily lead to incorrect assumptions even in these modern and near-modern structures, caution must be exercised when interpreting micro-organismal involvement in the construction of accretionary structures throughout the rock record.

Characterization of the first cultured free-living representative of Candidatus Izemoplasma uncovers its unique biology

Candidatus Izemoplasma, an intermediate in the reductive evolution from Firmicutes to Mollicutes, was proposed to represent a novel class of free-living wall-less bacteria within the phylum Tenericutes. Unfortunately, the paucity of pure cultures has limited further insights into their physiological and metabolic features as well as ecological roles. Here, we report the first successful isolation of an Izemoplasma representative from the deep-sea methane seep, strain zrk13, using a DNA degradation-driven method given Izemoplasma’s prominent DNA-degradation potentials. We further present a detailed description of the physiological, genomic and metabolic traits of the novel strain, which allows for the first time the reconstruction of the metabolic potential and lifestyle of a member of the tentatively defined Candidatus Izemoplasma. On the basis of the description of strain zrk13, the novel species and genus Xianfuyuplasma coldseepsis is proposed. Using a combined biochemical and transcriptomic method, we further show the supplement of organic matter, thiosulfate or bacterial genomic DNA could evidently promote the growth of strain zrk13. In particular, strain zrk13 could degrade and utilize the extracellular DNA for growth in both laboraterial and deep-sea conditions. Moreover, the predicted genes determining DNA-degradation broadly distribute in the genomes of other Izemoplasma members. Given that extracellular DNA is a particularly crucial phosphorus as well as nitrogen and carbon source for microorganisms in the seafloor, Izemoplasma bacteria are thought to be important contributors to the biogeochemical cycling in the deep ocean.

Wastewater treatment works change the intestinal microbiomes of insectivorous bats

Mammals, born with a near-sterile intestinal tract, are inoculated with their mothers’ microbiome during birth. Thereafter, extrinsic and intrinsic factors shape their intestinal microbe assemblage. Wastewater treatment works (WWTW), sites synonymous with pollutants and pathogens, receive influent from domestic, agricultural and industrial sources. The high nutrient content of wastewater supports abundant populations of chironomid midges (Diptera), which transfer these toxicants and potential pathogens to their predators, such as the banana bat Neoromicia nana (Vespertilionidae), thereby influencing their intestinal microbial assemblages. We used next generation sequencing and 16S rRNA gene profiling to identify and compare intestinal bacteria of N. nana at two reference sites and two WWTW sites. We describe the shared intestinal microbiome of the insectivorous bat, N. nana, consisting of seven phyla and eleven classes. Further, multivariate analyses revealed that location was the most significant driver (sex, body size and condition were not significant) of intestinal microbiome diversity. Bats at WWTW sites exhibited greater intestinal microbiota diversity than those at reference sites, likely due to wastewater exposure, stress and/or altered diet. Changes in their intestinal microbiota assemblages may allow these bats to cope with concomitant stressors.

Exploring the diversity of mechanosensitive channels in bacterial genomes

Mechanosensitive ion channels are responsible for touch sensation and proprioception in higher level organisms such as humans and recovery after osmotic stress in bacteria. Bacterial mechanosensitive channels are homologous to either the mechanosensitive channel of large conductance (MscL) or the mechanosensitive channel of small conductance (MscS). In the E. coli genome there are seven unique mechanosensitive channels, a single MscL homologue, and six MscS homologues. The six MscS homologues are members of the diverse MscS superfamily of ion channels, and these channels show variation on both the N and C termini when compared to E. coli MscS. In bacterial strains with phenotypic analysis of the endogenous mechanosensors, the quantity of MscS superfamily members in the genome range from 2 to 6 and all of the strains contain a copy of MscL. Here, we show an in-depth analysis of over 150 diverse bacterial genomes, encompassing nine phyla, to determine the number of genomes that contain an MscL homologue and the average number of MscS superfamily members per genome. We determined that the average genome contains 4 ± 3 MscS homologues and 67% of bacterial genomes encode for a MscL homologue.

Zeolite favours propionate syntrophic degradation during anaerobic digestion of food waste under low ammonia stress

Zeolite addition has been widely suggested for its ability to overcome ammonia stress occurring during anaerobic digestion. However little is known regarding the underlying mechanisms of mitigation and especially how zeolite influences the microbial structuration. The aim of this study was to bring new contributions on the effect of zeolite on the microbial community arrangement under a low ammonia stress. Replicated batch experiments were conducted. The microbial population was characterised with 16S sequencing. Methanogenic pathways were identified with methane isotopic fractionation. In presence of ammonia, zeolite mitigated the decrease of biogas production rate. Zeolite induced the development of Izimaplasmatales order and preserved Peptococcaceae family members, known as propionate degraders. Moreover methane isotopic fractionation showed that hydrogenotrophic methanogenesis was maintained in presence of zeolite under ammonia low stress. Our results put forward the benefit of zeolite to improve the bacteria-archaea syntrophy needed for propionate degradation and methane production under a low ammonia stress.

Network analysis and functional estimation of the microbiome reveal the effects of cashew nut shell liquid feeding on methanogen behaviour in the rumen

The effects of cashew nut shell liquid (CNSL) feeding on the methane (CH4 ) emission and the ruminal microbiome of Lai Sind beef cattle were investigated. Changes in the methane production and rumen microbiome by CNSL feeding were monitored by a respiration chamber and 16S rRNA gene amplicon sequencing respectively. The results demonstrated that CNSL feeding mitigated 20.2%-23.4% of the CH4 emission in vivo without apparent adverse effects on feed intake and feed digestibility. The rumen fluid analysis revealed a significant increase in the proportion of propionate in the total short-chain fatty acids. The relative abundance of methanogen (order Methanobacteriales) decreased significantly, indicating the direct inhibitory effect of CNSL on methanogens. The predicted function of the rumen microbiome indicated that carbohydrate and lipid metabolisms including propionate production were upregulated by CNSL feeding, whereas CH4 metabolism was downregulated. A network analysis revealed that methanogen changed its partner bacteria after CNSL feeding. The δ13 C of CH4 ranged from -74.2‰ to -66.6‰ with significant fluctuation by CNSL feeding, in agreement with the shift of the rumen microbiome. Our findings demonstrate that CNSL feeding can mitigate the CH4 emission from local cattle production systems in South-East Asia by modifying the rumen microbiome and its function.

Genomic Characterization of a Novel Tenericutes Bacterium from Deep-Sea Holothurian Intestine

Intestinal bacterial communities are highly relevant to the digestion, nutrition, growth, reproduction, and immunity of animals, but little is known about the composition and function of intestinal microbiota in deep-sea invertebrates. In this study, the intestinal microbiota of six holothurian Molpadia musculus were investigated, showing that their midguts were predominantly occupied by Izemoplasmatales bacteria. Using metagenomic sequencing, a draft genome of 1,822,181 bp was successfully recovered. After comparison with phylogenetically related bacteria, genes involved in saccharide usage and de novo nucleotide biosynthesis were reduced. However, a set of genes responsible for extracellular nucleoside utilization and 14 of 20 amino acid synthesis pathways were completely retained. Under oligotrophic condition, the gut-associated bacterium may make use of extracellular DNA for carbon and energy supplement, and may provide essential amino acids to the host. The clustered regularly interspaced short palindromic repeat (CRISPR) and restriction–modification (RM) systems presented in the genome may provide protection against invading viruses. A linear azol(in)e-containing peptide gene cluster for bacteriocin synthesize was also identified, which may inhibit the colonization and growth of harmful bacteria. Known virulence factors were not found by database searching. On the basis of its phylogenetic position and metabolic characteristics, we proposed that the bacterium represented a novel genus and a novel family within the Izemoplasmatales order and suggested it be named “Candidatus Bathyoplasma sp. NZ”. This was the first time describing host-associated Izemoplasmatales.

Species-dependent variation of the gut bacterial communities across Trypanosoma cruzi insect vectors

Triatomines (Hemiptera: Reduviidae) are the insect vectors of Trypanosoma cruzi, the causative agent of Chagas disease. The gut bacterial communities affect the development of T. cruzi inside the vector, making the characterization of its composition important in the understanding of infection development. We collected 54 triatomine bugs corresponding to four genera in different departments of Colombia. DNA extraction and PCR were performed to evaluate T. cruzi presence and to determine the discrete typing unit (DTU) of the parasite. PCR products of the bacterial 16S rRNA gene were pooled and sequenced. Resulting reads were denoised and QIIME 2 was used for the identification of amplicon sequence variants (ASVs). Diversity (alpha and beta diversity) and richness analyses, Circos plots, and principal component analysis (PCA) were also performed. The overall T. cruzi infection frequency was 75.9%, with TcI being the predominant DTU. Approximately 500,000 sequences were analyzed and 27 bacterial phyla were identified. The most abundant phyla were Proteobacteria (33.9%), Actinobacteria (32.4%), Firmicutes (19.6%), and Bacteroidetes (7.6%), which together accounted for over 90% of the gut communities identified in this study. Genera were identified for these main bacterial phyla, revealing the presence of important bacteria such as Rhodococcus, Serratia, and Wolbachia. The composition of bacterial phyla in the gut of the insects was significantly different between triatomine species, whereas no significant difference was seen between the state of T. cruzi infection. We suggest further investigation with the evaluation of additional variables and a larger sample size. To our knowledge, this study is the first characterization of the gut bacterial structure of the main triatomine genera in Colombia.

Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne

The use of straw for biofuel production is encouraged by the European Union. A previous study showed the feasibility of producing biomethane in upflow anaerobic sludge blanket (UASB) reactors using hydrolyzed, steam-pretreated wheat straw, before and after dark fermentation with Caldicellulosiruptor saccharolyticus, and lucerne. This study provides information on overall microbial community development in those UASB processes and changes related to acidification. The bacterial and archaeal community in granular samples was analyzed using high-throughput amplicon sequencing. Anaerobic digestion model no. 1 (ADM1) was used to predict the abundance of microbial functional groups. The sequencing results showed decreased richness and diversity in the microbial community, and decreased relative abundance of bacteria in relation to archaea, after process acidification. Canonical correspondence analysis showed significant negative correlations between the concentration of organic acids and three phyla, and positive correlations with seven phyla. Organic loading rate and total COD fed also showed significant correlations with microbial community structure, which changed over time. ADM1 predicted a decrease in acetate degraders after a decrease to pH ≤ 6.5. Acidification had a sustained effect on the microbial community and process performance.

Influence of the polar light cycle on seasonal dynamics of an Antarctic lake microbial community

BACKGROUND

Cold environments dominate the Earth's biosphere and microbial activity drives ecosystem processes thereby contributing greatly to global biogeochemical cycles. Polar environments differ to all other cold environments by experiencing 24-h sunlight in summer and no sunlight in winter. The Vestfold Hills in East Antarctica contains hundreds of lakes that have evolved from a marine origin only 3000-7000 years ago. Ace Lake is a meromictic (stratified) lake from this region that has been intensively studied since the 1970s. Here, a total of 120 metagenomes representing a seasonal cycle and four summers spanning a 10-year period were analyzed to determine the effects of the polar light cycle on microbial-driven nutrient cycles.

RESULTS

The lake system is characterized by complex sulfur and hydrogen cycling, especially in the anoxic layers, with multiple mechanisms for the breakdown of biopolymers present throughout the water column. The two most abundant taxa are phototrophs (green sulfur bacteria and cyanobacteria) that are highly influenced by the seasonal availability of sunlight. The extent of the Chlorobium biomass thriving at the interface in summer was captured in underwater video footage. The Chlorobium abundance dropped from up to 83% in summer to 6% in winter and 1% in spring, before rebounding to high levels. Predicted Chlorobium viruses and cyanophage were also abundant, but their levels did not negatively correlate with their hosts.

CONCLUSION

Over-wintering expeditions in Antarctica are logistically challenging, meaning insight into winter processes has been inferred from limited data. Here, we found that in contrast to chemolithoautotrophic carbon fixation potential of Southern Ocean Thaumarchaeota, this marine-derived lake evolved a reliance on photosynthesis. While viruses associated with phototrophs also have high seasonal abundance, the negative impact of viral infection on host growth appeared to be limited. The microbial community as a whole appears to have developed a capacity to generate biomass and remineralize nutrients, sufficient to sustain itself between two rounds of sunlight-driven summer-activity. In addition, this unique metagenome dataset provides considerable opportunity for future interrogation of eukaryotes and their viruses, abundant uncharacterized taxa (i.e. dark matter), and for testing hypotheses about endemic species in polar aquatic ecosystems. Video Abstract.

Role of microbial diversity for sustainable pyrite oxidation control in acid and metalliferous drainage prevention

Acid and metalliferous drainage (AMD) remains a challenging issue for the mining sector. AMD management strategies have attempted to shift from treatment of acid leachates post-generation to more sustainable at-source prevention. Here, the efficacy of microbial-geochemical at-source control approach was investigated over a period of 84 weeks. Diverse microbial communities were stimulated using organic carbon amendment in a simulated silicate-containing sulfidic mine waste rock environment. Mineral waste in the unamended leach system generated AMD quickly and throughout the study, with known lithotrophic iron- and sulfur-oxidising microbes dominating column communities. The organic-amended mineral waste column showed suppressed metal dissolution and AMD generation. Molecular DNA-based next generation sequencing confirmed a less diverse lithotrophic community in the acid-producing control, with a more diverse microbial community under organic amendment comprising organotrophic iron/sulfur-reducers, autotrophs, hydrogenotrophs and heterotrophs. Time-series multivariate statistical analyses displayed distinct ecological patterns in microbial diversity between AMD- and non-AMD-environments. Focused ion beam-TEM micrographs and elemental mapping showed that silicate-stabilised passivation layers were successfully established across pyrite surfaces in organic-amended treatments, with these layers absent in unamended controls. Organic amendment and resulting increases in microbial abundance and diversity played an important role in sustaining these passivating layers in the long-term.

Lists of names of prokaryotic Candidatus taxa

We here present annotated lists of names of Candidatus taxa of prokaryotes with ranks between subspecies and class, proposed between the mid-1990s, when the provisional status of Candidatus taxa was first established, and the end of 2018. Where necessary, corrected names are proposed that comply with the current provisions of the International Code of Nomenclature of Prokaryotes and its Orthography appendix. These lists, as well as updated lists of newly published names of Candidatus taxa with additions and corrections to the current lists to be published periodically in the International Journal of Systematic and Evolutionary Microbiology, may serve as the basis for the valid publication of the Candidatus names if and when the current proposals to expand the type material for naming of prokaryotes to also include gene sequences of yet-uncultivated taxa is accepted by the International Committee on Systematics of Prokaryotes.

Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli

Background

The metabolic capacity, stress response and evolution of uncultured environmental Tenericutes have remained elusive, since previous studies have been largely focused on pathogenic species. In this study, we expanded analyses on Tenericutes lineages that inhabit various environments using a collection of 840 genomes.

Results

Several environmental lineages were discovered inhabiting the human gut, ground water, bioreactors and hypersaline lake and spanning the Haloplasmatales and Mycoplasmatales orders. A phylogenomics analysis of Bacilli and Tenericutes genomes revealed that some uncultured Tenericutes are affiliated with novel clades in Bacilli, such as RF39, RFN20 and ML615. Erysipelotrichales and two major gut lineages, RF39 and RFN20, were found to be neighboring clades of Mycoplasmatales. We detected habitat-specific functional patterns between the pathogenic, gut and the environmental Tenericutes, where genes involved in carbohydrate storage, carbon fixation, mutation repair, environmental response and amino acid cleavage are overrepresented in the genomes of environmental lineages, perhaps as a result of environmental adaptation. We hypothesize that the two major gut lineages, namely RF39 and RFN20, are probably acetate and hydrogen producers. Furthermore, deteriorating capacity of bactoprenol synthesis for cell wall peptidoglycan precursors secretion is a potential adaptive strategy employed by these lineages in response to the gut environment.

Conclusions

This study uncovers the characteristic functions of environmental Tenericutes and their relationships with Bacilli, which sheds new light onto the pathogenicity and evolutionary processes of Mycoplasmatales.

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.

Effect of sulfate addition on carbon flow and microbial community composition during thermophilic digestion of cellulose

Substrates with high sulfate levels pose problems for biogas production as they allow sulfate reducing bacteria to compete with syntrophic and methanogenic members of the community. In addition, the end product of sulfate reduction, hydrogen sulfide, is toxic and corrosive. Here we show how sulfate addition affects physiological processes in a thermophilic methanogenic system by analyzing the carbon flow and the microbial community with quantitative PCR and amplicon sequencing of the 16s rRNA gene. A sulfate addition of 0.5 to 3 g/L caused a decline in methane production by 73-92%, while higher sulfate concentrations had no additional inhibitory effect. Generally, sulfate addition induced a shift in the composition of the microbial community towards a higher dominance of Firmicutes and decreasing abundances of Bacteroidetes and Euryarchaeota. The abundance of methanogens (e.g., Methanoculleus and Methanosarcina) was reduced, while sulfate reducing bacteria (especially Candidatus Desulforudis and Desulfotomaculum) increased significantly in presence of sulfate. The sulfate addition had a significant impact on the carbon flow within the system, shifting the end product from methane and carbon dioxide to acetate and carbon dioxide. Interestingly, methane production quickly resumed, when sulfate was no longer present in the system. Despite the strong impact of sulfate addition on the carbon flow and the microbial community structure during thermophilic biogas production, short-term process disturbances caused by unexpected introduction of sulfate may be overcome due to the high resilience of the engaged microorganisms.

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.

A timetree for phytoplasmas (Mollicutes) with new insights on patterns of evolution and diversification

The first comprehensive timetree is presented for phytoplasmas, a diverse group of obligate intracellular bacteria restricted to phloem sieve elements of vascular plants and tissues of their hemipteran insect vectors. Maximum likelihood-based phylogenetic analysis of DNA sequence data from the 16S rRNA and methionine aminopeptidase (map) genes yielded well resolved estimates of phylogenetic relationships among major phytoplasma lineages, 16Sr groups and known strains of phytoplasmas. Age estimates for divergences among two major lineages of Mollicutes based on a previous comprehensive bacterial timetree were used to calibrate an initial 16S timetree. A separate timetree was estimated based on the more rapidly-evolving map gene, with an internal calibration based on a recent divergence within two related 16Sr phytoplasma subgroups in group 16SrV thought to have been driven by the introduction of the North American leafhopper vector Scaphoideus titanus Ball into Europe during the early part of the 20th century. Combining the resulting divergence time estimates into a final 16S timetree suggests that evolutionary rates have remained relatively constant overall through the evolution of phytoplasmas and that the origin of this lineage, at ~641 million years ago (Ma), preceded the origin of land plants and hemipteran insects. Nevertheless, the crown group of phytoplasmas is estimated to have begun diversifying ~316 Ma, roughly coinciding with the origin of seed plants and Hemiptera. Some phytoplasma groups apparently associated with particular plant families or insect vector lineages generally arose more recently than their respective hosts and vectors, suggesting that vector-mediated host shifts have been an important mechanism in the evolutionary diversification of phytoplasmas. Further progress in understanding macroevolutionary patterns in phytoplasmas is hindered by large gaps in knowledge of the identity of competent vectors and lack of data on phytoplasma associations with non-economically important plants.

Long-Term Mesophilic Anaerobic Co-Digestion of Swine Manure with Corn Stover and Microbial Community Analysis

Long-term anaerobic co-digestion of swine manure (SM) and corn stover (CS) was conducted using semi-continuously loaded digesters under mesophilic conditions. A preliminary test was first conducted to test the effects of loading rates, and results indicated the 3 g-VS L⁻¹ d⁻¹ was the optimal loading rate. Based on the preliminary results, a verification replicated test was conducted with 3 g-VS L⁻¹ d⁻¹ loading rate and different SM/CS ratios (1:1, 2:1 and 1:2). Results showed that a SM/CS ratio of 2/1 was optimal, based on maximum observed methane-VS_des generation and carbon conversion efficiency (72.56 ± 3.40 mL g⁻¹ and 40.59%, respectively). Amplicon sequencing analysis suggested that microbial diversity was increased with CS loading. Amino-acid-degrading bacteria were abundant in the treatment groups. Archaea Methanoculleus could enhance biogas and methane productions.

Oligosaccharides from Morinda officinalis Slow the Progress of Aging Mice by Regulating the Key Microbiota-Metabolite Pairs

The gut microbiota is considered an important factor in the progression of Alzheimer's disease (AD). Active research on the association between the metabolome and the gut microbiome is ongoing and can provide a large amount of beneficial information about the interactions between the microbiome and the metabolome. Previous studies have shown that the oligosaccharides from Morinda officinalis (OMO) can delay the progress of AD in model animals by regulating the diversity of the gut microbiome and metabolic components, and the correlation between the gut microbiome and metabolic components still needs to be further verified. This study applied a new two-level strategy to investigate and ensure the accuracy and consistency of the results. This strategy can be used to determine the association between the gut microbiome and serum metabolome in APP/PS1 transgenic mice and C57BL/6J male mice. The “4C0d-2 spp.-Cholesterol,” “CW040 spp.-L-valine,” “CW040 spp.-L-acetylcarnitine,” “RF39 spp.-L-valine,” “TM7-3 spp.-L-valine,” and “TM7-3 spp.-L-acetylcarnitine” associations among specific “microbiota-metabolite” pairs were further identified based on univariate and multivariate correlation analyses and functional analyses. The key relevant pairs were verified by an independent oligosaccharide intervention study, and the gut microbiome and serum metabolome of the OMO intervention group were similar to those of the normal group. The results indicate that OMO can significantly suppress Alzheimer's disease by regulating the key microbiota-metabolite pairs. Therefore, this two-level strategy is effective in identifying the principal correlations in large datasets obtained from combinations of multiomic studies and further enhancing our understanding of the correlation between the brain and gut in patients with AD.

Cumulative impact of long-term intensive mariculture on total and active bacterial communities in the core sediments of the Ailian Bay, North China

The exponential growth of off-shore mariculture worldwide over the last 20 years has had significant impact on coastal sediment biogeochemistry. However, there are no long-term records of the cumulative impacts of mariculture on the benthic bacterial community. Here, total (DNA) and active (RNA) bacterial community compositions were characterized using MiSeq sequencing of 16S rRNA gene in four core sediments of the Ailian Bay, one of the typical intensive mariculture areas in China with more than fifty-year history of kelp and scallop cultivation. The γ-Proteobacteria, δ-Proteobacteria, Acidobacteria and Acitinobacteria were more abundant in the total bacterial communities, while β-Proteobacteria, Anaerolineae, Clostridia, Spirochaetes and Cyanobacteria were enriched in the active bacterial communities. Significant differences were observed between total and active benthic bacterial communities. The influences of different mariculture modes on the total bacterial communities were more significant than those on the active bacterial communities. Only limited groups of the total bacterial communities were significant influenced by the cumulative effects of the long-term mariculture. The bacterial genera with the function in the sulfide cycling and organic consumption were enriched in the total bacterial population of the integrated multi-trophic aquaculture (IMTA) areas. The variations of both total and active bacterial communities were significantly influenced by grain sizes, total organic carbon and nutrients. Both total and active bacterial communities exhibited a slightly stronger response to environmental factors than to spatial (distance) factors. The effects of mutualism might dominate the total and active bacterial networks in the Ailian Bay. The present study demonstrated that the cumulative influences of the long-term and intensive IMTA mariculture on total benthic bacterial communities in the sub-surface sediments of the Ailian Bay were stronger than those on the active benthic bacterial communities, which provided some insights into the potential ecological roles of specific taxa in the sediments of the IMTA ecosystems.

Shotgun Metagenomics Reveals the Benthic Microbial Community Response to Plastic and Bioplastic in a Coastal Marine Environment

Plastic is incredibly abundant in marine environments but little is known about its effects on benthic microbiota and biogeochemical cycling. This study reports the shotgun metagenomic sequencing of biofilms fouling plastic and bioplastic microcosms staged at the sediment–water interface of a coastal lagoon. Community composition analysis revealed that plastic biofilms were indistinguishable in comparison to a ceramic biofilm control. By contrast, bioplastic biofilms were distinct and dominated by sulfate-reducing microorganisms (SRM). Analysis of bioplastic gene pools revealed the enrichment of esterases, depolymerases, adenylyl sulfate reductases (aprBA), and dissimilatory sulfite reductases (dsrAB). The nearly 20-fold enrichment of a phylogenetically diverse polyhydroxybutyrate (PHB) depolymerase suggests this gene was distributed across a mixed microbial assemblage. The metagenomic reconstruction of genomes identified novel species of Desulfovibrio, Desulfobacteraceae, and Desulfobulbaceae among the abundant SRM, and these genomes contained genes integral to both bioplastic degradation and sulfate reduction. Findings indicate that bioplastic promoted a rapid and significant shift in benthic microbial diversity and gene pools, selecting for microbes that participate in bioplastic degradation and sulfate reduction. If plastic pollution is traded for bioplastic pollution and sedimentary inputs are large, the microbial response could unintentionally affect benthic biogeochemical activities through the stimulation of sulfate reducers.

Contrasting community composition of endospores and vegetative Firmicutes in a marine sediment suggests both endogenous and exogenous sources of endospore accumulation

Bacterial endospores are highly abundant in marine sediments, but their taxonomic identity and ecology is largely unknown. We selectively extracted DNA from endospores and vegetative cells and sequenced 16S rRNA genes to characterize the composition of the endospore and vegetative Firmicutes communities in the sediment and water column of Aarhus Bay (Denmark). The endospore community in the sediment was dominated by the families Bacillaceae, Lachnospiraceae, Clostridiaceae and Ruminoccocaceae. These families were also represented in the vegetative community in the sediment and the endospore community in the water column. OTUs of high relative abundance in the endospore community were also represented in the vegetative Firmicutes community. Other OTUs were exclusively found in the endospore communities. This suggests that endospores accumulate in marine sediments due to passive deposition from the water column and sporulation of vegetative cells in the sediment. Some OTUs were detected in the endospore community of the water column and the vegetative community the sediment indicating that endospores deposited from the water column may germinate upon burial/deposition in the sediment. We provide novel insight into the composition of endospore communities in marine sediments and highlight their role in microbial dispersal and as a seed bank in subsurface sediments.

Microbial diversity of an Antarctic subglacial community and high-resolution replicate sampling inform hydrological connectivity in a polar desert

Antarctic subglacial environments host microbial ecosystems and are proving to be geochemically and biologically diverse. The Taylor Glacier, Antarctica, periodically expels iron-rich brine through a conduit sourced from a deep subglacial aquifer, creating a dramatic red surface feature known as Blood Falls. We used Illumina MiSeq sequencing to describe the core microbiome of this subglacial brine and identified previously undetected but abundant groups including the candidate bacterial phylum Atribacteria and archaeal phylum Pacearchaeota. Our work represents the first microbial characterization of samples collected from within a glacier using a melt probe, and the only Antarctic subglacial aquatic environment that, to date, has been sampled twice. A comparative analysis showed the brine community to be stable at the operational taxonomic unit level of 99% identity over a decade. Higher resolution sequencing enabled deconvolution of the microbiome of subglacial brine from mixtures of materials collected at the glacier surface. Diversity patterns between this brine and samples from the surrounding landscape provide insight into the hydrological connectivity of subglacial fluids to the surface polar desert environment. Understanding subice brines collected on the surfaces of thick ice covers has implications for analyses of expelled materials that may be sampled on icy extraterrestrial worlds.

Effects of metal and metalloid pollutants on the microbiota composition of feces obtained from twelve commercial pig farms across China

Understanding the metal and metalloid contamination and microbiota composition of pig feces is an important step required to support the design and implementation of effective pollution control and prevention strategies. A survey was implemented in 12 locations across China to investigate the content of metals and metalloids, and the main composition of the microbial communities of commercially reared pigs during two growth periods, defined as the early (Q group) and the later fattening growth phases (H group). These data showed widespread Al, Mn, Cu, Zn, and Fe pollution in pig feces. The concentration of Zn in the Q group feces was nearly two times higher than the levels measured in the H group. The microbial composition of the Q group exhibited greater richness of operational taxonomic units (OTUs) and fewer bacteria associated with zoonotic diseases compared with the microbial composition of the H group. Spearman rank correlation analysis showed that Cu and northern latitudes had a significant positive effect on the richness of bacterial communities in pig feces. Zn and Cd exhibited the biggest impact on microbial community composition based on canonical correspondence analysis. Functional metagenomic prediction indicated that about 0.8% genes present in the pig feces bacteria community are related to human diseases, and significantly more predicted pathogenic genes were detected in the H group than in the Q group. These results support the need to monitor heavy metal contamination and to control for zoonotic pathogens disseminated from pig feces in Chinese pig farms.

k-mer Similarity, Networks of Microbial Genomes, and Taxonomic Rank

Microbial genomes have been shaped by parent-to-offspring (vertical) descent and lateral genetic transfer. These processes can be distinguished by alignment-based inference and comparison of phylogenetic trees for individual gene families, but this approach is not scalable to whole-genome sequences, and a tree-like structure does not adequately capture how these processes impact microbial physiology. Here we adopted alignment-free approaches based on k-mer statistics to infer phylogenomic networks involving 2,783 completely sequenced bacterial and archaeal genomes and compared the contributions of rRNA, protein-coding, and plasmid sequences to these networks. Our results show that the phylogenomic signal arising from ribosomal RNAs is strong and extends broadly across all taxa, whereas that from plasmids is strong but restricted to closely related groups, particularly Proteobacteria. However, the signal from the other chromosomal regions is restricted in breadth. We show that mean k-mer similarity can correlate with taxonomic rank. We also link the implicated k-mers to genome annotation (thus, functions) and define core k-mers (thus, core functions) in specific phyletic groups. Highly conserved functions in most phyla include amino acid metabolism and transport as well as energy production and conversion. Intracellular trafficking and secretion are the most prominent core functions among Spirochaetes, whereas energy production and conversion are not highly conserved among the largely parasitic or commensal Tenericutes. These observations suggest that differential conservation of functions relates to niche specialization and evolutionary diversification of microbes. Our results demonstrate that k-mer approaches can be used to efficiently identify phylogenomic signals and conserved core functions at the multigenome scale. IMPORTANCE Genome evolution of microbes involves parent-to-offspring descent, and lateral genetic transfer that convolutes the phylogenomic signal. This study investigated phylogenomic signals among thousands of microbial genomes based on short subsequences without using multiple-sequence alignment. The signal from ribosomal RNAs is strong across all taxa, and the signal of plasmids is strong only in closely related groups, particularly Proteobacteria. However, the signal from other chromosomal regions (∼99% of the genomes) is remarkably restricted in breadth. The similarity of subsequences is found to correlate with taxonomic rank and informs on conserved and differential core functions relative to niche specialization and evolutionary diversification of microbes. These results provide a comprehensive, alignment-free view of microbial genome evolution as a network, beyond a tree-like structure.

A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments

BACKGROUND

Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic sequencing on soda lake sediments to give the first extensive overview of the taxonomic diversity found in these complex, extreme environments and to gain novel physiological insights into the most abundant, uncultured prokaryote lineages.

RESULTS

We sequenced five metagenomes obtained from four surface sediments of Siberian soda lakes with a pH 10 and a salt content between 70 and 400 g L^-1. The recovered 16S rRNA gene sequences were mostly from Bacteria, even in the salt-saturated lakes. Most OTUs were assigned to uncultured families. We reconstructed 871 metagenome-assembled genomes (MAGs) spanning more than 45 phyla and discovered the first extremophilic members of the Candidate Phyla Radiation (CPR). Five new species of CPR were among the most dominant community members. Novel dominant lineages were found within previously well-characterized functional groups involved in carbon, sulfur, and nitrogen cycling. Moreover, key enzymes of the Wood-Ljungdahl pathway were encoded within at least four bacterial phyla never previously associated with this ancient anaerobic pathway for carbon fixation and dissimilation, including the Actinobacteria.

CONCLUSIONS

Our first sequencing effort of hypersaline soda lake sediment metagenomes led to two important advances. First, we showed the existence and obtained the first genomes of haloalkaliphilic members of the CPR and several hundred other novel prokaryote lineages. The soda lake CPR is a functionally diverse group, but the most abundant organisms in this study are likely fermenters with a possible role in primary carbon degradation. Second, we found evidence for the presence of the Wood-Ljungdahl pathway in many more taxonomic groups than those encompassing known homo-acetogens, sulfate-reducers, and methanogens. Since only few environmental metagenomics studies have targeted sediment microbial communities and never to this extent, we expect that our findings are relevant not only for the understanding of haloalkaline environments but can also be used to set targets for future studies on marine and freshwater sediments.

Development and characterization of stable anaerobic thermophilic methanogenic microbiomes fermenting switchgrass at decreasing residence times

BACKGROUND

Anaerobic fermentation of lignocellulose occurs in both natural and managed environments, and is an essential part of the carbon cycle as well as a promising route to sustainable production of fuels and chemicals. Lignocellulose solubilization by mixed microbiomes is important in these contexts.

RESULTS

Here, we report the development of stable switchgrass-fermenting enrichment cultures maintained at various residence times and moderately high (55 °C) temperatures. Anaerobic microbiomes derived from a digester inoculum were incubated at 55 °C and fed semi-continuously with medium containing 30 g/L mid-season harvested switchgrass to achieve residence times (RT) of 20, 10, 5, and 3.3 days. Stable, time-invariant cellulolytic methanogenic cultures with minimal accumulation of organic acids were achieved for all RTs. Fractional carbohydrate solubilization was 0.711, 0.654, 0.581 and 0.538 at RT = 20, 10, 5 and 3.3 days, respectively, and glucan solubilization was proportional to xylan solubilization at all RTs. The rate of solubilization was described well by the equation r = k(C - C₀f_r), where C represents the concentration of unutilized carbohydrate, C₀ is the concentration of carbohydrate (cellulose and hemicellulose) entering the bioreactor and f_r is the extrapolated fraction of entering carbohydrate that is recalcitrant at infinite residence time. The 3.3 day RT is among the shortest RT reported for stable thermophilic, methanogenic digestion of a lignocellulosic feedstock. 16S rDNA phylotyping and metagenomic analyses were conducted to characterize the effect of RT on community dynamics and to infer functional roles in the switchgrass to biogas conversion to the various microbial taxa. Firmicutes were the dominant phylum, increasing in relative abundance from 54 to 96% as RT decreased. A Clostridium clariflavum strain with genetic markers for xylose metabolism was the most abundant lignocellulose-solubilizing bacterium. A Thermotogae (Defluviitoga tunisiensis) was the most abundant bacterium in switchgrass digesters at RT = 20 days but decreased in abundance at lower RTs as did multiple Chloroflexi. Synergistetes and Euryarchaeota were present at roughly constant levels over the range of RTs examined.

CONCLUSIONS

A system was developed in which stable methanogenic steady-states were readily obtained with a particulate biomass feedstock, mid-season switchgrass, at laboratory (1 L) scale. Characterization of the extent and rate of carbohydrate solubilization in combination with 16S rDNA and metagenomic sequencing provides a multi-dimensional view of performance, species composition, glycoside hydrolases, and metabolic function with varying residence time. These results provide a point of reference and guidance for future studies and organism development efforts involving defined cultures.

Draft Genome Sequence of "Candidatus Izimaplasma sp." Strain ZiA1, Obtained from a Toluene-Degrading and Iron-Reducing Enrichment Culture

Here, we report the draft genome sequence of “Candidatus Izimaplasma sp.” strain ZiA1 (1.88 Mb and 29.6% G+C content).

Here, we report the draft genome sequence of “Candidatus Izimaplasma sp.” strain ZiA1 (1.88 Mb and 29.6% G+C content). Strain ZiA1 was cocultured with iron-reducing and toluene-degrading bacteria in an enrichment culture from tidal flat sediment. Like the genomes of other strains of “Ca. Izimaplasma,” the ZiA1 genome contained genes required for anaerobic fermentation.

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Taxonomy is an organizing principle of biology and is ideally based on evolutionary relationships among organisms. Development of a robust bacterial taxonomy has been hindered by an inability to obtain most bacteria in pure culture and, to a lesser extent, by the historical use of phenotypes to guide classification. Culture-independent sequencing technologies have matured sufficiently that a comprehensive genome-based taxonomy is now possible. We used a concatenated protein phylogeny as the basis for a bacterial taxonomy that conservatively removes polyphyletic groups and normalizes taxonomic ranks on the basis of relative evolutionary divergence. Under this approach, 58% of the 94,759 genomes comprising the Genome Taxonomy Database had changes to their existing taxonomy. This result includes the description of 99 phyla, including six major monophyletic units from the subdivision of the Proteobacteria, and amalgamation of the Candidate Phyla Radiation into a single phylum. Our taxonomy should enable improved classification of uncultured bacteria and provide a sound basis for ecological and evolutionary studies.