Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities

Metabolic exchanges are ubiquitous in natural microbial communities

Microbial communities drive global biogeochemical cycles and shape the health of plants and animals-including humans. Their structure and function are determined by ecological and environmental interactions that govern the assembly, stability and evolution of microbial communities. A widely held view is that antagonistic interactions such as competition predominate in microbial communities and are ecologically more important than synergistic interactions-for example, mutualism or commensalism. Over the past decade, however, a more nuanced picture has emerged, wherein bacteria, archaea and fungi exist within interactive networks in which they exchange essential and non-essential metabolites. These metabolic interactions profoundly impact not only the physiology, ecology and evolution of the strains involved, but are also central to the functioning of many, if not all, microbiomes. Therefore, we advocate for a balanced view of microbiome ecology that encompasses both synergistic and antagonistic interactions as key forces driving the structure and dynamics within microbial communities.

Microplastic ingestion affects hydrogen production and microbiomes in the gut of the terrestrial isopod Porcellio scaber

Microplastic (MP) is an environmental burden and enters food webs via ingestion by macrofauna, including isopods (Porcellio scaber) in terrestrial ecosystems. Isopods represent ubiquitously abundant, ecologically important detritivores. However, MP-polymer specific effects on the host and its gut microbiota are unknown. We tested the hypothesis that biodegradable (polylactic acid [PLA]) and non-biodegradable (polyethylene terephthalate [PET]; polystyrene [PS]) MPs have contrasting effects on P. scaber mediated by changes of the gut microbiota. The isopod fitness after an 8-week MP-exposure was generally unaffected, although the isopods showed avoidance behaviour to PS-food. MP-polymer specific effects on gut microbes were detected, including a stimulation of microbial activity by PLA compared with MP-free controls. PLA stimulated hydrogen emission from isopod guts, while PET and PS were inhibitory. We roughly estimated 107  kg year-1 hydrogen emitted from the isopods globally and identified their guts as anoxic, significant mobile sources of reductant for soil microbes despite the absence of classical obligate anaerobes, likely due to Enterobacteriaceae-related fermentation activities that were stimulated by lactate generated during PLA-degradation. The findings suggest negative effects of PET and PS on gut fermentation, modulation of important isopod hydrogen emissions by MP pollution and the potential of MP to affect terrestrial food webs.

Influence of soil nutrients on the presence and distribution of CPR bacteria in a long-term crop rotation experiment

Bacteria affiliated with the Candidate Phyla Radiation (CPR) are a hyper-diverse group of ultra-small bacteria with versatile yet sparse metabolisms. However, most insights into this group come from a surprisingly small number of environments, and recovery of CPR bacteria from soils has been hindered due to their extremely low abundance within complex microbial assemblages. In this study we enriched soil samples from 14 different soil fertility treatments for ultra-small (<0.45 μm) bacteria in order to study rare soil CPR. 42 samples were sequenced, enabling the reconstruction of 27 quality CPR metagenome-assembled genomes (MAGs) further classified as Parcubacteria/Paceibacteria, Saccharibacteria/Saccharimonadia and ABY1, in addition to representative genomes from Gemmatimonadetes, Dependentiae and Chlamydae phyla. These genomes were fully annotated and used to reconstruct the CPR community across all 14 plots. Additionally, for five of these plots, the entire microbiota was reconstructed using 16S amplification, showing that specific soil CPR may form symbiotic relationships with a varied and circumstantial range of hosts. Cullars CPR had a prevalence of enzymes predicted to degrade plant-derived carbohydrates, which suggests they have a role in plant biomass degradation. Parcubacteria appear to be more apt at microfauna necromass degradation. Cullars Saccharibacteria and a Parcubacteria group were shown to carry a possible aerotolerance mechanism coupled with potential for aerobic respiration, which appear to be a unique adaptation to the oxic soil environment. Reconstruction of CPR communities across treatment plots showed that they were not impacted by changes in nutrient levels or microbiota composition, being only impacted by extreme conditions, causing some CPR to dominate the community. These findings corroborate the understanding that soil-dwelling CPR bacteria have a very broad symbiont range and have metabolic capabilities associated to soil environments which allows them to scavenge resources and form resilient communities. The contributions of these microbial dark matter species to soil ecology and plant interactions will be of significant interest in future studies.

Effects of SMOF on soil properties, root-zone microbial community structure, metabolites, and maize (Zea mays L.) response on a reclaimed barren mountainous land

Introduction

Maize is the largest crop produced in China. With the growing population and the rapid development of urbanization and industrialization, maize has been recently cultivated in reclaimed barren mountainous lands in Zhejiang Province, China. However, the soil is usually not suitable for cultivation because of its low pH and poor nutrient conditions. To improve soil quality for crop growth, various fertilizers, including inorganic, organic, and microbial fertilizers, were used in the field. Among them, organic fertilizer-based sheep manure greatly improved the soil quality and has been widely adopted in reclaimed barren mountainous lands. But the mechanism of action was not well clear.

Methods

The field experiment (SMOF, COF, CCF and the control) was carried out on a reclaimed barren mountainous land in Dayang Village, Hangzhou City, Zhejiang Province, China. To systematically evaluate the effect of SMOF on reclaimed barren mountainous lands, soil properties, the root-zone microbial community structure, metabolites, and maize response were investigated.

Results

Compared with the control, SMOF could not significantly affect the soil pH but caused 46.10%, 28.28%, 101.94%, 56.35%, 79.07%, and 76.07% increases in the OMC, total N, available P, available K, MBC, and MBN, respectively. Based on 16S amplicon sequencing of soil bacteria, compared with the control, SMOF caused a 11.06-334.85% increase in the RA of Ohtaekwangia, Sphingomonas, unclassified_Sphingomonadaceae, and Saccharibacteria and a 11.91-38.60% reduction in the RA of Spartobacteria, Gemmatimonas, Gp4, Flavisolibacter, Subdivision3, Gp6, and unclassified_Betaproteobacteria, respectively. Moreover, based on ITS amplicon sequencing of soil fungi, SMOF also caused a 42.52-330.86% increase in the RA of Podospora, Clitopilus, Ascobolus, Mortierella, and Sordaria and a 20.98-64.46% reduction in the RA of Knufia, Fusarium, Verticillium, and Gibberella, respectively, compared with the control. RDA of microbial communities and soil properties revealed that the main variables of bacterial and fungal communities included available K, OMC, available P, MBN, and available K, pH, and MBC, respectively. In addition, LC-MS analysis indicated that 15 significant DEMs belonged to benzenoids, lipids, organoheterocyclic compounds, organic acids, phenylpropanoids, polyketides, and organic nitrogen compounds in SMOF and the control group, among which four DEMs were significantly correlated with two genera of bacteria and 10 DEMs were significantly correlated with five genera of fungi. The results revealed complicated interactions between microbes and DEMs in the soil of the maize root zone. Furthermore, the results of field experiments demonstrated that SMOF could cause a significant increase in maize ears and plant biomass.

Conclusions

Overall, the results of this study showed that the application of SMOF not only significantly modified the physical, chemical, and biological properties of reclaimed barren mountainous land but also promoted maize growth. SMOF can be used as a good amendment for maize production in reclaimed barren mountainous lands.

Sensitive or tolerant functional microorganisms under cadmium stress: suggesting potential specific interaction network characteristics in the rhizosphere system of karst potato

The heavy metal cadmium (Cd) pollution in Chinese karst soils threatens food security, and microorganisms play an important role in regulating the migration and transformation of Cd in the soil-plant system. Nevertheless, the interaction characteristics between key microbial communities and environmental factors in response to Cd stress in specific crop environmental systems need to be explored. In this study, the soil (ferralsols)-microbe-crop (potato) system was taken as the object to explore the potato rhizosphere microbiome, using toxicology and molecular biology approaches, to explore the potato rhizosphere soil properties, microbial stress characteristics, and important microbial taxa under Cd stress. We hypothesized that different members of fungal and bacterial microbiome would regulate the resilience of potato rhizosphere and plants to Cd stress in the soil environment. Meanwhile, individual taxa will have different roles in the contaminated rhizosphere ecosystem. We found that soil pH was the main environmental factor affecting fungal community structure; urea-decomposing and nitrate-reducing functional bacteria as well as endosymbiotic and saprophytic functional fungi gradually decreased. In particular, Basidiomycota may play a key role in preventing the migration of Cd from the soil to plants (potato). These findings provide important candidates for screening the cascade of Cd inhibition (detoxification/regulation) from soil to microorganisms to plants. Our work provides an important foundation and research insights for the application of microbial remediation technology in the karst cadmium-contaminated farmland.

Physiology of the tongue with emphasis on taste transduction

The tongue is a complex multifunctional organ that interacts and senses both interoceptively and exteroceptively. Although it is easily visible to almost all of us, it is relatively understudied and what is in the literature is often contradictory or is not comprehensively reported. The tongue is both a motor and a sensory organ: motor in that it is required for speech and mastication, and sensory in that it receives information to be relayed to the central nervous system pertaining to the safety and quality of the contents of the oral cavity. Additionally, the tongue and its taste apparatus form part of an innate immune surveillance system. For example, loss or alteration in taste perception can be an early indication of infection as became evident during the present global SARS-CoV-2 pandemic. Here, we particularly emphasize the latest updates in the mechanisms of taste perception, taste bud formation and adult taste bud renewal, and the presence and effects of hormones on taste perception, review the understudied lingual immune system with specific reference to SARS-CoV-2, discuss nascent work on tongue microbiome, as well as address the effect of systemic disease on tongue structure and function, especially in relation to taste.

Updated Virophage Taxonomy and Distinction from Polinton-like Viruses

Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of "hyperparasitism" in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and taxonomy of this group of viruses. Specifically, virophages have been linked in the literature to other "virophage-like" mobile genetic elements and viruses, including polinton-like viruses (PLVs), but there are no formal demarcation criteria and proper nomenclature for either group, i.e., virophage or PLVs. Here, as part of the ICTV Virophage Study Group, we leverage a large set of genomes gathered from published datasets as well as newly generated protist genomes to propose delineation criteria and classification methods at multiple taxonomic ranks for virophages 'sensu stricto', i.e., genomes related to the prototype isolates Sputnik and mavirus. Based on a combination of comparative genomics and phylogenetic analyses, we show that this group of virophages forms a cohesive taxon that we propose to establish at the class level and suggest a subdivision into four orders and seven families with distinctive ecogenomic features. Finally, to illustrate how the proposed delineation criteria and classification method would be used, we apply these to two recently published datasets, which we show include both virophages and other virophage-related elements. Overall, we see this proposed classification as a necessary first step to provide a robust taxonomic framework in this area of the virosphere, which will need to be expanded in the future to cover other virophage-related viruses such as PLVs.

Gut microbiota facilitates adaptation of the plateau zokor (Myospalax baileyi) to the plateau living environment

Gut microbiota not only helps the hosts to perform many key physiological functions such as food digestion, energy harvesting and immune regulation, but also influences host ecology and facilitates adaptation of the host to extreme environments. Plateau zokors epitomize successful physiological adaptation to their living environment in the face of the harsh environment characterized by low temperature, low pressure and hypoxia in the Tibetan plateau region and high concentrations of CO₂ in their burrows. Therefore, here we used a metagenomic sequencing approach to explore how gut microbiota contributed to the adaptive evolution of the plateau zokor on the Qinghai-Tibet Plateau. Our metagenomic results show that the gut microbiota of plateau zokors on the Tibetan plateau is not only enriched in a large number of species related to energy metabolism and production of short-chain fatty acids (SCFAs), but also significantly enriched the KO terms that involve carbohydrate uptake pathways, which well address energy uptake in plateau zokors while also reducing inflammatory responses due to low pressure, hypoxia and high CO₂ concentrations. There was also a significant enrichment of tripeptidyl-peptidase II (TPPII) associated with antigen processing, apoptosis, DNA damage repair and cell division, which may facilitate the immune response and tissue damage repair in plateau zokors under extreme conditions. These results suggest that these gut microbiota and their metabolites together contribute to the physiological adaptation of plateau zokors, providing new insights into the contribution of the microbiome to the evolution of mammalian adaptation.

Candidate Phyla Radiation, an Underappreciated Division of the Human Microbiome, and Its Impact on Health and Disease

Candidate phyla radiation (CPR) is an emerging division of the bacterial domain within the human microbiota. Still poorly known, these microorganisms were first described in the environment in 1981 as "ultramicrobacteria" with a cell volume under 0.1 μm³ and were first associated with the human oral microbiota in 2007. The evolution of technology has been paramount for the study of CPR within the human microbiota. In fact, since these ultramicrobacteria have yet to be axenically cultured despite ongoing efforts, progress in imaging technology has allowed their observation and morphological description. Although their genomic abilities and taxonomy are still being studied, great strides have been made regarding their taxonomic classification, as well as their lifestyle. In addition, advancements in next-generation sequencing and the continued development of bioinformatics tools have allowed their detection as commensals in different human habitats, including the oral cavity and gastrointestinal and genital tracts, thus highlighting CPR as a nonnegligible part of the human microbiota with an impact on physiological settings. Conversely, several pathologies present dysbiosis affecting CPR levels, including inflammatory, mucosal, and infectious diseases. In this exhaustive review of the literature, we provide a historical perspective on the study of CPR, an overview of the methods available to study these organisms and a description of their taxonomy and lifestyle. In addition, their distribution in the human microbiome is presented in both homeostatic and dysbiotic settings. Future efforts should focus on developing cocultures and, if possible, axenic cultures to obtain isolates and therefore genomes that would provide a better understanding of these ultramicrobacteria, the importance of which in the human microbiome is undeniable.

Effect of ancient Khorasan wheat on gut microbiota, inflammation, and short-chain fatty acid production in patients with fibromyalgia

BACKGROUND

Fibromyalgia (FM) syndrome is mainly characterized by widespread pain, sleeping disorders, fatigue, and cognitive dysfunction. In many cases, gastrointestinal distress is also reported, suggesting the potential pathogenic role of the gut microbiota (GM). The GM is deeply influenced by several environmental factors, especially the diet, and recent findings highlighted significant symptom improvement in FM patients following various nutritional interventions such as vegetarian diet, low-fermentable oligosaccharides, disaccharides, monosaccharides, and polyols based diets, gluten-free diet, and especially an ancient grain supplementation. In particular, a recent study reported that a replacement diet with ancient Khorasan wheat led to an overall improvement in symptom severity of FM patients.

AIM

To examine the effects of ancient Khorasan wheat on the GM, inflammation, and short-chain fatty acid production in FM patients.

METHODS

After a 2-wk run-in period, 20 FM patients were enrolled in this randomized, double-blind crossover trial. In detail, they were assigned to consume either Khorasan or control wheat products for 8 wk and then, following an 8-wk washout period, crossed. Before and after treatments, GM characterization was performed by 16S rRNA sequencing while the fecal molecular inflammatory response and the short-chain fatty acids (SCFAs) were respectively determined with the Luminex MAGPIX detection system and a mass chromatography-mass spectrometry method.

RESULTS

The Khorasan wheat replacement diet, in comparison with the control wheat diet, had more positive effects on intestinal microbiota composition and on both the fecal immune and SCFAs profiles such as the significant increase of butyric acid levels (P = 0.054), candidatus Saccharibacteria (P = 9.95e-06) and Actinobacteria, and the reduction of Enterococcaceae (P = 4.97e-04). Moreover, the improvement of various FM symptoms along with the variation of some gut bacteria after the Khorasan wheat diet have been documented; in fact we reported positive correlations between Actinobacteria and both Tiredness Symptoms Scale (P < 0.001) and Functional Outcome of Sleep Questionnaire (P < 0.05) scores, between Verrucomicrobiae and both Widespread Pain Index (WPI) + Symptom Severity scale (SS) (P < 0.05) and WPI (P < 0.05) scores, between candidatus Saccharibacteria and SS score (P < 0.05), and between Bacteroidales and Sleep-Related and Safety Behaviour Questionnaire score (P < 0.05).

CONCLUSION

The replacement diet based on ancient Khorasan wheat results in beneficial GM compositional and functional modifications that positively correlate with an improvement of FM symptomatology.

Assessment of Physicochemical, Microbiological and Toxicological Hazards at an Illegal Landfill in Central Poland

This study aimed to assess the physicochemical, microbiological and toxicological hazards at an illegal landfill in central Poland. The research included the analysis of airborne dust (laser photometer), the number of microorganisms in the air, soil and leachate (culture method) and the microbial diversity in the landfill environment (high-throughput sequencing on the Illumina Miseq); the cytotoxicity (PrestoBlue) and genotoxicity (alkaline comet assay) of soil and leachate were tested. Moreover, an analysis of UHPLC-Q-ToF-UHRMS (ultra-high-performance liquid chromatography-quadrupole-time-of-flight ultrahigh-resolution mass spectrometry) was performed to determine the toxic compounds and microbial metabolites. The PM₁ dust fraction constituted 99.89% and 99.99% of total dust and exceeded the threshold of 0.025 mg m⁻³ at the tested locations. In the air, the total number of bacteria was 9.33 × 10¹–1.11 × 10³ CFU m⁻³, while fungi ranged from 1.17 × 10² to 4.73 × 10² CFU m⁻³. Psychrophilic bacteria were detected in the largest number in leachates (3.3 × 10⁴ to 2.69 × 10⁶ CFU mL⁻¹) and in soil samples (8.53 × 10⁵ to 1.28 × 10⁶ CFU g⁻¹). Bacteria belonging to Proteobacteria (42–64.7%), Bacteroidetes (4.2–23.7%), Actinobacteria (3.4–19.8%) and Firmicutes (0.7–6.3%) dominated. In the case of fungi, Basidiomycota (23.3–27.7%), Ascomycota (5.6–46.3%) and Mortierellomycota (3.1%) have the highest abundance. Bacteria (Bacillus, Clostridium, Cellulosimicrobium, Escherichia, Pseudomonas) and fungi (Microascus, Chrysosporium, Candida, Malassezia, Aspergillus, Alternaria, Fusarium, Stachybotrys, Cladosporium, Didymella) that are potentially hazardous to human health were detected in samples collected from the landfill. Tested leachates and soils were characterised by varied cyto/genotoxins. Common pesticides (carbamazepine, prometryn, terbutryn, permethrin, carbanilide, pyrethrin, carbaryl and prallethrin), quaternary ammonium compounds (benzalkonium chlorides), chemicals and/or polymer degradation products (melamine, triphenylphosphate, diphenylphtalate, insect repellent diethyltoluamide, and drugs (ketoprofen)) were found in soil and leachate samples. It has been proven that the tested landfill is the source of the emission of particulate matter; microorganisms (including potential pathogens) and cyto/genotoxic compounds.

A Genomic Perspective Across Earth's Microbiomes Reveals That Genome Size in Archaea and Bacteria Is Linked to Ecosystem Type and Trophic Strategy

Our view of genome size in Archaea and Bacteria has remained skewed as the data has been dominated by genomes of microorganisms that have been cultivated under laboratory settings. However, the continuous effort to catalog Earth's microbiomes, specifically propelled by recent extensive work on uncultivated microorganisms, provides an opportunity to revise our perspective on genome size distribution. We present a meta-analysis that includes 26,101 representative genomes from 3 published genomic databases; metagenomic assembled genomes (MAGs) from GEMs and stratfreshDB, and isolates from GTDB. Aquatic and host-associated microbial genomes present on average the smallest estimated genome sizes (3.1 and 3.0 Mbp, respectively). These are followed by terrestrial microbial genomes (average 3.7 Mbp), and genomes from isolated microorganisms (average 4.3 Mbp). On the one hand, aquatic and host-associated ecosystems present smaller genomes sizes in genera of phyla with genome sizes above 3 Mbp. On the other hand, estimated genome size in phyla with genomes under 3 Mbp showed no difference between ecosystems. Moreover, we observed that when using 95% average nucleotide identity (ANI) as an estimator for genetic units, only 3% of MAGs cluster together with genomes from isolated microorganisms. Although there are potential methodological limitations when assembling and binning MAGs, we found that in genome clusters containing both environmental MAGs and isolate genomes, MAGs were estimated only an average 3.7% smaller than isolate genomes. Even when assembly and binning methods introduce biases, estimated genome size of MAGs and isolates are very similar. Finally, to better understand the ecological drivers of genome size, we discuss on the known and the overlooked factors that influence genome size in different ecosystems, phylogenetic groups, and trophic strategies.

Power Play of Commensal Bacteria in the Buccal Cavity of Female Nile Tilapia

Fish are widely exposed to higher microbial loads compared to land and air animals. It is known that the microbiome plays an essential role in the health and development of the host. The oral microbiome is vital in females of different organisms, including the maternal mouthbrooding species such as Nile tilapia (Oreochromis niloticus). The present study reports for the first time the microbial composition in the buccal cavity of female and male Nile tilapia reared in a recirculating aquaculture system. Mucus samples were collected from the buccal cavity of 58 adult fish (∼1 kg), and 16S rRNA gene amplicon sequencing was used to profile the microbial communities in females and males. The analysis revealed that opportunistic pathogens such as Streptococcus sp. were less abundant in the female buccal cavity. The power play of certain bacteria such as Acinetobacter, Acidobacteria (GP4 and GP6), and Saccharibacteria that have known metabolic advantages was evident in females compared to males. Association networks inferred from relative abundances showed few microbe–microbe interactions of opportunistic pathogens in female fish. The findings of opportunistic bacteria and their interactions with other microbes will be valuable for improving Nile tilapia rearing practices. The presence of bacteria with specific functions in the buccal cavity of female fish points to their ability to create a protective microbial ecosystem for the offspring.

Bacterial Communities Associated with Poa annua Roots in Central European (Poland) and Antarctic Settings (King George Island)

Poa annua (annual bluegrass) is one of the most ubiquitous grass species in the world. In isolated regions of maritime Antarctica, it has become an invasive organism threatening native tundra communities. In this study, we have explored and compared the rhizosphere and root-endosphere dwelling microbial community of P. annua specimens of maritime Antarctic and Central European origin in terms of bacterial phylogenetic diversity and microbial metabolic activity with a geochemical soil background. Our results show that the rhizospheric bacterial community was unique for each sampling site, yet the endosphere communities were similar to each other. However, key plant-associated bacterial taxa such as the Rhizobiaceae family were poorly represented in Antarctic samples, probably due to high salinity and heavy metal concentrations in the soil. Metabolic activity in the Antarctic material was considerably lower than in Central European samples. Antarctic root endosphere showed unusually high numbers of certain opportunistic bacterial groups, which proliferated due to low competition conditions. Thirteen bacterial families were recognized in this study to form a core microbiome of the P. annua root endosphere. The most numerous were the Flavobacteriaceae, suspected to be major contributors to the ecological success of annual bluegrass, especially in harsh, Antarctic conditions.