Evolutionary Implications of Anoxygenic Phototrophy in the Bacterial Phylum Candidatus Eremiobacterota (WPS-2)

Unravelling the influence of microplastics with/without additives on radish (Raphanus sativus) and microbiota in two agricultural soils differing in pH

Here we investigated the effects of three types of microplastics (MPs), i.e., PS (P), ABS (B), PVC (V), and each with additive (MPAs) (PA, BA, and VA), on soil health, microbial community, and plant growth in two acidic and slightly alkaline soils. Incubation experiment revealed that although MPs and MPAs consistently stimulated soil nutrients and heavy metals (e.g., Mn, Cu) in weakly alkaline soils, only BA and VA led to increase in soil nutrients and heavy metals in acidic soils. This suggests distinct response patterns in the two soils depending on their initial pH. Concerning microorganisms, MPs and MPAs reduced the assembly degree of bacteria in acidic soils, with a reduction of Chloroflexi and Acidobacteriota but an increase of WPS-2 in VA. Culture experiment showed consistent positive or negative responses in radish seed germination, roots, and antioxidant activity across MPs and MPAs types in both soils, while the responses of seed heavy metals (e.g., Cr, Cd) were consistent in acidic soils but dependent on MPs and MPAs types in alkaline soils. Therefore, our study strongly suggests that the effects of MPs on soil-microbial-plant systems were highly dependent on initial soil characteristics and the types of MPs with plastic additives.

Boreal moss-microbe interactions are revealed through metagenome assembly of novel bacterial species

Moss-microbe interactions contribute to ecosystem processes in boreal forests. Yet, how host-specific characteristics and the environment drive the composition and metabolic potential of moss microbiomes is still poorly understood. In this study, we use shotgun metagenomics to identify the taxonomy and metabolic potential of the bacteria of four moss species of the boreal forests of Northern Québec, Canada. To characterize moss bacterial community composition and diversity, we assembled the genomes of 110 potentially novel bacterial species. Our results highlight that moss genus, species, gametophyte section, and to a lesser extent soil pH and soil temperature, drive moss-associated bacterial community composition and diversity. In the brown gametophyte section, two Stigonema spp. showed partial pathway completeness for photosynthesis and nitrogen fixation, while all brown-associated Hyphomicrobiales had complete assimilatory nitrate reduction pathways and many nearly complete carbon fixation pathways. Several brown-associated species showed partial to complete pathways for coenzyme M and F420 biosynthesis, important for methane metabolism. In addition, green-associated Hyphomicrobiales (Methylobacteria spp.) displayed potential for the anoxygenic photosystem II pathway. Overall, our findings demonstrate how host-specific characteristics and environmental factors shape the composition and metabolic potential of moss bacteria, highlighting their roles in carbon fixation, nitrogen cycling, and methane metabolism in boreal forests.

Exploring the Origins and Evolution of Oxygenic and Anoxygenic Photosynthesis in Deeply Branched Cyanobacteriota

Cyanobacteriota, the sole prokaryotes capable of oxygenic photosynthesis (OxyP), occupy a unique and pivotal role in Earth's history. While the notion that OxyP may have originated from Cyanobacteriota is widely accepted, its early evolution remains elusive. Here, by using both metagenomics and metatranscriptomics, we explore 36 metagenome-assembled genomes from hot spring ecosystems, belonging to two deep-branching cyanobacterial orders: Thermostichales and Gloeomargaritales. Functional investigation reveals that Thermostichales encode the crucial thylakoid membrane biogenesis protein, vesicle-inducing protein in plastids 1 (Vipp1). Based on the phylogenetic results, we infer that the evolution of the thylakoid membrane predates the divergence of Thermostichales from other cyanobacterial groups and that Thermostichales may be the most ancient lineage known to date to have inherited this feature from their common ancestor. Apart from OxyP, both lineages are potentially capable of sulfide-driven AnoxyP by linking sulfide oxidation to the photosynthetic electron transport chain. Unexpectedly, this AnoxyP capacity appears to be an acquired feature, as the key gene sqr was horizontally transferred from later-evolved cyanobacterial lineages. The presence of two D1 protein variants in Thermostichales suggests the functional flexibility of photosystems, ensuring their survival in fluctuating redox environments. Furthermore, all MAGs feature streamlined phycobilisomes with a preference for capturing longer-wavelength light, implying a unique evolutionary trajectory. Collectively, these results reveal the photosynthetic flexibility in these early-diverging cyanobacterial lineages, shedding new light on the early evolution of Cyanobacteriota and their photosynthetic processes.

Pioneer plants enhance soil multifunctionality by reshaping underground multitrophic community during natural succession of an abandoned rare earth mine tailing

Spontaneous natural succession in metal mine tailings is fundamental to the rehabilitation of bare tailing. Here, an abandoned rare earth element (REE) mine tailing with spontaneous colonisation by pioneer plants with different functional traits was selected. Soil nutrient cycling, fertility, organic matter decomposition as well as underground organismal communities and their multitrophic networks were investigated. Compared with the bare tailing, the colonisation with Lycopodium japonicum, Miscanthus sinensis, and Dicranopteris dichotoma increased soil multifunction by 222%, 293%, and 525%, respectively. This was accompanied by significant changes in soil bacterial and protistan community composition and increased soil multitrophic network complexity. Rhizospheres of different plant species showed distinct microbial community composition compared to that of bare tailing. Some WPS-2, Chloroflexi, and Chlorophyta were mainly present in the bare tailing, while some Proteobacteria and Cercozoa were predominantly seen in the rhizosphere. Pearson correlation and Random Forest revealed the biotic factors driving soil multifunction. Structural equation modelling further revealed that pioneer plants improved soil multifunction primarily by decreasing the microbial biodiversity and increasing the multitrophic network complexity. Overall, this highlights the importance of subterrestrial organisms in accelerating soil rehabilitation during natural succession and provides options for the ecological restoration of degraded REE mining areas.

Illuminating the coevolution of photosynthesis and Bacteria

Life harnessing light energy transformed the relationship between biology and Earth-bringing a massive flux of organic carbon and oxidants to Earth's surface that gave way to today's organotrophy- and respiration-dominated biosphere. However, our understanding of how life drove this transition has largely relied on the geological record; much remains unresolved due to the complexity and paucity of the genetic record tied to photosynthesis. Here, through holistic phylogenetic comparison of the bacterial domain and all photosynthetic machinery (totally spanning >10,000 genomes), we identify evolutionary congruence between three independent biological systems-bacteria, (bacterio)chlorophyll-mediated light metabolism (chlorophototrophy), and carbon fixation-and uncover their intertwined history. Our analyses uniformly mapped progenitors of extant light-metabolizing machinery (reaction centers, [bacterio]chlorophyll synthases, and magnesium-chelatases) and enzymes facilitating the Calvin-Benson-Bassham cycle (form I RuBisCO and phosphoribulokinase) to the same ancient Terrabacteria organism near the base of the bacterial domain. These phylogenies consistently showed that extant phototrophs ultimately derived light metabolism from this bacterium, the last phototroph common ancestor (LPCA). LPCA was a non-oxygen-generating (anoxygenic) phototroph that already possessed carbon fixation and two reaction centers, a type I analogous to extant forms and a primitive type II. Analyses also indicate chlorophototrophy originated before LPCA. We further reconstructed evolution of chlorophototrophs/chlorophototrophy post-LPCA, including vertical inheritance in Terrabacteria, the rise of oxygen-generating chlorophototrophy in one descendant branch near the Great Oxidation Event, and subsequent emergence of Cyanobacteria. These collectively unveil a detailed view of the coevolution of light metabolism and Bacteria having clear congruence with the geological record.

Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities

Microbes represent the most common organisms on Earth; however, less than 2% of microbial species in the environment can undergo cultivation for study under laboratory conditions, and the rest of the enigmatic, microbial world remains mysterious, constituting a kind of "microbial dark matter" (MDM). In the last two decades, remarkable progress has been made in culture-dependent and culture-independent techniques. More recently, studies of MDM have relied on culture-independent techniques to recover genetic material through either unicellular genomics or shotgun metagenomics to construct single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), respectively, which provide information about evolution and metabolism. Despite the remarkable progress made in the past decades, the functional diversity of MDM still remains uncharacterized. This review comprehensively summarizes the recently developed culture-dependent and culture-independent techniques for characterizing MDM, discussing major challenges, opportunities, and potential applications. These activities contribute to expanding our knowledge of the microbial world and have implications for various fields including Biotechnology, Bioprospecting, Functional genomics, Medicine, Evolutionary and Planetary biology. Overall, this review aims to peel off the layers from MDM, shed light on recent advancements, identify future challenges, and illuminate the exciting opportunities that lie ahead in unraveling the secrets of this intriguing microbial realm.

The diversification and potential function of microbiome in sediment-water interface of methane seeps in South China Sea

The sediment-water interfaces of cold seeps play important roles in nutrient transportation between seafloor and deep-water column. Microorganisms are the key actors of biogeochemical processes in this interface. However, the knowledge of the microbiome in this interface are limited. Here we studied the microbial diversity and potential metabolic functions by 16S rRNA gene amplicon sequencing at sediment-water interface of two active cold seeps in the northern slope of South China Sea, Lingshui and Site F cold seeps. The microbial diversity and potential functions in the two cold seeps are obviously different. The microbial diversity of Lingshui interface areas, is found to be relatively low. Microbes associated with methane consumption are enriched, possibly due to the large and continuous eruptions of methane fluids. Methane consumption is mainly mediated by aerobic oxidation and denitrifying anaerobic methane oxidation (DAMO). The microbial diversity in Site F is higher than Lingshui. Fluids from seepage of Site F are mitigated by methanotrophic bacteria at the cyclical oxic-hypoxic fluctuating interface where intense redox cycling of carbon, sulfur, and nitrogen compounds occurs. The primary modes of microbial methane consumption are aerobic methane oxidation, along with DAMO, sulfate-dependent anaerobic methane oxidation (SAMO). To sum up, anaerobic oxidation of methane (AOM) may be underestimated in cold seep interface microenvironments. Our findings highlight the significance of AOM and interdependence between microorganisms and their environments in the interface microenvironments, providing insights into the biogeochemical processes that govern these unique ecological systems.

Functional guilds and drivers of diversity in seaweed-associated bacteria

Comparisons of functional and taxonomic profiles from bacterial communities in different habitats have suggested the existence of functional guilds composed of taxonomically or phylogenetically distinct members. Such guild membership is, however, rarely defined and the factors that drive functional diversity in bacteria remain poorly understood. We used seaweed-associated bacteria as a model to shed light on these important aspects of community ecology. Using a large dataset of over 1300 metagenome-assembled genomes from 13 seaweed species we found substantial overlap in the functionality of bacteria coming from distinct taxa, thus supporting the existence of functional guilds. This functional equivalence between different taxa was particularly pronounced when only functions involved in carbohydrate degradation were considered. We further found that bacterial taxonomy is the dominant driver of functional differences between bacteria and that seaweed species or seaweed type (i.e. brown, red and green) had relatively stronger impacts on genome functionality for carbohydrate-degradation functions when compared to all other cellular functions. This study provides new insight into the factors underpinning the functional diversity of bacteria and contributes to our understanding how community function is generated from individual members.

Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle

Photosynthesis is a fundamental biogeochemical process, thought to be restricted to a few bacterial and eukaryotic phyla. However, understanding the origin and evolution of phototrophic organisms can be impeded and biased by the difficulties of cultivation. Here, we analyzed metagenomic datasets and found potential photosynthetic abilities encoded in the genomes of uncultivated bacteria within the phylum Myxococcota. A putative photosynthesis gene cluster encoding a type-II reaction center appears in at least six Myxococcota families from three classes, suggesting vertical inheritance of these genes from an early common ancestor, with multiple independent losses in other lineages. Analysis of metatranscriptomic datasets indicate that the putative myxococcotal photosynthesis genes are actively expressed in various natural environments. Furthermore, heterologous expression of myxococcotal pigment biosynthesis genes in a purple bacterium supports that the genes can drive photosynthetic processes. Given that predatory abilities are thought to be widespread across Myxococcota, our results suggest the intriguing possibility of a chimeric lifestyle (combining predatory and photosynthetic abilities) in members of this phylum.

New insight into the effect of microplastics on antibiotic resistance and bacterial community of biofilm

Microplastics (MPs) could serve as substrates for microbial colonization and biofilm formation. However, research on the effects of different types of microplastics and natural substrates on biofilm formation and community structure in the presence of antibiotic-resistant bacteria (ARB) is limited. In this study, we employed by means of microcosm experiments to analyze the situation of biofilms conditions, bacterial resistance patterns, antibiotic resistance genes (ARGs) distribution, and bacterial community on different substrates using microbial cultivation, high throughtput sequencing and PCR. The result showed that biofilms on different substrates markedly increased with time, with MPs surfaces formed more biofilm than stone. Analyses of antibiotic resistant showed negligible differences in the resistance rate to the same antibiotic at 30 d, but tetB would be selectively enriched on PP and PET. The microbial communities associated with biofilms on MPs and stones exhibited variations during different stages of formation. Notably, phylum WPS-2 and Epsilonbacteraeota were identified as the dominant microbiomes of biofilms on MPs and stones at 30 d, respectively. Correlation analysis suggested that WPS-2 could potentially be a tetracycline-resistant bacterium, while Epsilonbacteraeota did not correlate with any detected ARB. Our results emphasized the potential threat posed by MPs as attachment carriers for bacteria, particularly ARB, in aquatic environments.

Wastewater from textile digital printing as a substrate for microalgal growth and valorization

This study aims at evaluating an innovative biotechnological process for the concomitant bioremediation and valorization of wastewater from textile digital printing technology based on a microalgae/bacteria consortium. Nutrient and colour removal were assessed in lab-scale batch and continuous experiments and the produced algae/bacteria biomass was characterized for pigment content and biomethane potential. Microbial community analysis provided insight of the complex community structure responsible for the bioremediation action. Specifically, a community dominated by Scenedesmus spp. and xenobiotic and dye degrading bacteria was naturally selected in continuous photobioreactors. Data confirm the ability of the microalgae/bacteria consortium to grow in textile wastewater while reducing the nutrient content and colour. Improvement strategies were eventually identified to foster biomass growth and process performances. The experimental findings pose the basis of the integration of a microalgal-based process into the textile sector in a circular economy perspective.

Changes of Soil Dissolved Organic Matter and Its Relationship with Microbial Community along the Hailuogou Glacier Forefield Chronosequence

Glacier-retreated areas are ideal areas to study soil biogeochemical processes during vegetation succession, because of the limited effect of other environmental and climatic factors. In this study, the changes of soil dissolved organic matter (DOM) and its relationship with microbial communities along the Hailuogou Glacier forefield chronosequence were investigated. Both microbial diversity and DOM molecular chemodiversity recovered rapidly at the initial stage, indicating the pioneering role of microorganisms in soil formation and development. The chemical stability of soil organic matter enhanced with vegetation succession due to the retaining of compounds with high oxidation state and aromaticity. The molecular composition of DOM affected microbial communities, while microorganisms tended to utilize labile components to form refractory components. This complex relationship network between microorganisms and DOM components played an important role in the development of soil organic matter as well as the formation of stable soil carbon pool in glacier-retreated areas.

Diversity dynamics of aerobic anoxygenic phototrophic bacteria in a freshwater lake

Aerobic anoxygenic photoheterotrophic (AAP) bacteria represent a functional group of prokaryotic organisms that harvests light energy using bacteriochlorophyll-containing photosynthetic reaction centers. They represent an active and rapidly growing component of freshwater bacterioplankton, with the highest numbers observed usually in summer. Species diversity of freshwater AAP bacteria has been studied before in lakes, but its seasonal dynamics remain unknown. In this report, we analysed temporal changes in the composition of the phototrophic community in an oligo-mesotrophic freshwater lake using amplicon sequencing of the pufM marker gene. The AAP community was dominated by phototrophic Gammaproteobacteria and Alphaproteobacteria, with smaller contribution of phototrophic Chloroflexota and Gemmatimonadota. Phototrophic Eremiobacteriota or members of Myxococcota were not detected. Interestingly, some AAP taxa, such as Limnohabitans, Rhodoferax, Rhodobacterales or Rhizobiales, were permanently present over the sampling period, while others, such as Sphingomonadales, Rhodospirillales or Caulobacterales appeared only transiently. The environmental factors that best explain the seasonal changes in AAP community were temperature, concentrations of oxygen and dissolved organic matter.

Vulcanimicrobium alpinus gen. nov. sp. nov., the first cultivated representative of the candidate phylum "Eremiobacterota", is a metabolically versatile aerobic anoxygenic phototroph

The previously uncultured phylum "Candidatus Eremiobacterota" is globally distributed and often abundant in oligotrophic environments. Although it includes lineages with the genetic potential for photosynthesis, one of the most important metabolic pathways on Earth, the absence of pure cultures has limited further insights into its ecological and physiological traits. We report the first successful isolation of a "Ca. Eremiobacterota" strain from a fumarolic ice cave on Mt. Erebus volcano (Antarctica). Polyphasic analysis revealed that this organism is an aerobic anoxygenic photoheterotrophic bacterium with a unique lifestyle, including bacteriochlorophyll a production, CO2 fixation, a high CO2 requirement, and phototactic motility using type IV-pili, all of which are highly adapted to polar and fumarolic environments. The cells are rods or filaments with a vesicular type intracytoplasmic membrane system. The genome encodes novel anoxygenic Type II photochemical reaction centers and bacteriochlorophyll synthesis proteins, forming a deeply branched monophyletic clade distinct from known phototrophs. The first cultured strain of the eighth phototrophic bacterial phylum which we name Vulcanimicrobium alpinus gen. nov., sp. nov. advances our understanding of ecology and evolution of photosynthesis.

Brain-gut-liver axis: Chronic psychological stress promotes liver injury and fibrosis via gut in rats

Background

The effect of chronic psychological stress on hepatitis and liver fibrosis is concerned. However, its mechanism remains unclear. We investigated the effect and mechanism of chronic psychological stress in promoting liver injury and fibrosis through gut.

Methods

Sixty male SD rats were randomly assigned to 6 groups. Rat models of chronic psychological stress (4 weeks) and liver fibrosis (8 weeks) were established. The diversity of gut microbiota in intestinal feces, permeability of intestinal mucosa, pathologies of intestinal and liver tissues, collagen fibers, protein expressions of toll-like receptor 4 (TLR4), myeloid differentiation factor 88 (MyD88), nuclear factor kappa β (NF-κβ), tumor necrosis factor α (TNF-α) and interleukin 1 (IL-1) in liver tissue, liver function and coagulation function in blood and lipopolysaccharide (LPS) in portal vein blood were detected and analyzed.

Results

The diversities and abundances of gut microbiota were significant differences in rats among each group. The pathological lesions of intestinal and liver tissues, decreased expression of occludin protein in intestinal mucosa, deposition of collagen fibers and increased protein expression of TLR4, MyD88, NF-κβ, TNF-α and IL-1 in liver tissue, increased LPS level in portal vein blood, and abnormalities of liver function and coagulation function, were observed in rats exposed to chronic psychological stress or liver fibrosis. There were significant differences with normal rats. When the dual intervention factors of chronic psychological stress and liver fibrosis were superimposed, the above indicators were further aggravated.

Conclusion

Chronic psychological stress promotes liver injury and fibrosis, depending on changes in the diversity of gut microbiota and increased intestinal permeability caused by psychological stress, LPS that enters liver and acts on TLR4, and active LPS-TLR4 pathway depend on MyD88. It demonstrates the possibility of existence of brain-gut-liver axis.

Stability and volatility shape the gut bacteriome and Kazachstania slooffiae dynamics in preweaning, nursery and adult pigs

The gut microbiome plays important roles in the maintenance of health and pathogenesis of diseases in the growing host. In order to fully comprehend the interplay of the gut microbiome and host, a foundational understanding of longitudinal microbiome, including bacteria and fungi, development is necessary. In this study, we evaluated enteric microbiome and host dynamics throughout the lifetime of commercial swine. We collected a total of 234 fecal samples from ten pigs across 31 time points in three developmental stages (5 preweaning, 15 nursery, and 11 growth adult). We then performed 16S rRNA gene amplicon sequencing for bacterial profiles and qPCR for the fungus Kazachstania slooffiae. We identified distinct bacteriome clustering according to the host developmental stage, with the preweaning stage exhibiting low bacterial diversity and high volatility amongst samples. We further identified clusters of bacteria that were considered core, increasing, decreasing or stage-associated throughout the host lifetime. Kazachstania slooffiae was absent in the preweaning stage but peaked during the nursery stage of the host. We determined that all host growth stages contained negative correlations between K. slooffiae and bacterial genera, with only the growth adult stage containing positive correlates. Our stage-associated bacteriome results suggested the neonate contained a volatile gut microbiome. Upon weaning, the microbiome became relatively established with comparatively fewer perturbations in microbiome composition. Differential analysis indicated bacteria might play distinct stage-associated roles in metabolism and pathogenesis. The lack of positive correlates and shared K. slooffiae-bacteria interactions between stages warranted future research into the interactions amongst these kingdoms for host health. This research is foundational for understanding how bacteria and fungi develop singularly, as well as within a complex ecosystem in the host's gut environment.

Biogeographical survey of soil microbiomes across sub-Saharan Africa: structure, drivers, and predicted climate-driven changes

BACKGROUND

Top-soil microbiomes make a vital contribution to the Earth's ecology and harbor an extraordinarily high biodiversity. They are also key players in many ecosystem services, particularly in arid regions of the globe such as the African continent. While several recent studies have documented patterns in global soil microbial ecology, these are largely biased towards widely studied regions and rely on models to interpolate the microbial diversity of other regions where there is low data coverage. This is the case for sub-Saharan Africa, where the number of regional microbial studies is very low in comparison to other continents.

RESULTS

The aim of this study was to conduct an extensive biogeographical survey of sub-Saharan Africa's top-soil microbiomes, with a specific focus on investigating the environmental drivers of microbial ecology across the region. In this study, we sampled 810 sample sites across 9 sub-Saharan African countries and used taxonomic barcoding to profile the microbial ecology of these regions. Our results showed that the sub-Saharan nations included in the study harbor qualitatively distinguishable soil microbiomes. In addition, using soil chemistry and climatic data extracted from the same sites, we demonstrated that the top-soil microbiome is shaped by a broad range of environmental factors, most notably pH, precipitation, and temperature. Through the use of structural equation modeling, we also developed a model to predict how soil microbial biodiversity in sub-Saharan Africa might be affected by future climate change scenarios. This model predicted that the soil microbial biodiversity of countries such as Kenya will be negatively affected by increased temperatures and decreased precipitation, while the fungal biodiversity of Benin will benefit from the increase in annual precipitation.

CONCLUSION

This study represents the most extensive biogeographical survey of sub-Saharan top-soil microbiomes to date. Importantly, this study has allowed us to identify countries in sub-Saharan Africa that might be particularly vulnerable to losses in soil microbial ecology and productivity due to climate change. Considering the reliance of many economies in the region on rain-fed agriculture, this study provides crucial information to support conservation efforts in the countries that will be most heavily impacted by climate change. Video Abstract.

(Meta)Genomic Analysis Reveals Diverse Energy Conservation Strategies Employed by Globally Distributed Gemmatimonadota

Gemmatimonadota is a phylum-level lineage distributed widely but rarely reported. Only six representatives of Gemmatimonadota have so far been isolated and cultured in laboratory. The physiology, ecology, and evolutionary history of this phylum remain unknown. The 16S rRNA gene survey of our salt lake and deep-sea sediments, and Earth Microbiome Project (EMP) samples, reveals that Gemmatimonadota exist in diverse environments globally. In this study, we retrieved 17 metagenome-assembled genomes (MAGs) from salt lake sediments (12 MAGs) and deep-sea sediments (5 MAGs). Analysis of these MAGs and the nonredundant MAGs or genomes from public databases reveals Gemmatimonadota can degrade various complex organic substrates, and mainly employ heterotrophic pathways (e.g., glycolysis and tricarboxylic acid [TCA] cycle) for growth via aerobic respiration. And the processes of sufficient energy being stored in glucose through gluconeogenesis, followed by the synthesis of more complex compounds, are prevalent in Gemmatimonadota. A highly expandable pangenome for Gemmatimonadota has been observed, which presumably results from their adaptation to thriving in diverse environments. The enrichment of the Na⁺/H⁺ antiporter in the SG8-23 order represents their adaptation to salty habitats. Notably, we identified a novel lineage of the SG8-23 order, which is potentially anoxygenic phototrophic. This lineage is not closely related to the phototrophs in the order of Gemmatimonadales. The two orders differ distinctly in the gene organization and phylogenetic relationship of their photosynthesis gene clusters, indicating photosystems in Gemmatimonadota have evolved in two independent routes.

IMPORTANCE The phylum Gemmatimonadota is widely distributed in various environments. However, their physiology, ecology and evolutionary history remain unknown, primary due to the limited cultured isolates and available genomes. We were intrigued to find out how widespread this phylum is, and how it can thrive under diverse conditions. Our results here expand the knowledge of the genetic and metabolic diversity of Gemmatimonadota, and shed light on the diverse energy conservation strategies (i.e., oxidative phosphorylation, substrate phosphorylation, and photosynthetic phosphorylation) responsible for their global distribution. Moreover, gene organization and phylogenetic analysis of photosynthesis gene clusters in Gemmatimonadota provide a valuable insight into the evolutionary history of photosynthesis.

Temperature and Geographic Location Impact the Distribution and Diversity of Photoautotrophic Gene Variants in Alkaline Yellowstone Hot Springs

Alkaline hot springs in Yellowstone National Park (YNP) provide a framework to study the relationship between photoautotrophs and temperature. Previous work has focused on studying how cyanobacteria (oxygenic phototrophs) vary with temperature, sulfide, and pH, but many questions remain regarding the ecophysiology of anoxygenic photosynthesis due to the taxonomic and metabolic diversity of these taxa. To this end, we examined the distribution of genes involved in phototrophy, carbon fixation, and nitrogen fixation in eight alkaline (pH 7.3-9.4) hot spring sites near the upper temperature limit of photosynthesis (71ºC) in YNP using metagenome sequencing. Based on genes encoding key reaction center proteins, geographic isolation plays a larger role than temperature in selecting for distinct phototrophic Chloroflexi, while genes typically associated with autotrophy in anoxygenic phototrophs, did not have distinct distributions with temperature. Additionally, we recovered Calvin cycle gene variants associated with Chloroflexi, an alternative carbon fixation pathway in anoxygenic photoautotrophs. Lastly, we recovered several abundant nitrogen fixation gene sequences associated with Roseiflexus, providing further evidence that genes involved in nitrogen fixation in Chloroflexi are more common than previously assumed. Together, our results add to the body of work on the distribution and functional potential of phototrophic bacteria in Yellowstone National Park hot springs and support the hypothesis that a combination of abiotic and biotic factors impact the distribution of phototrophic bacteria in hot springs. Future studies of isolates and metagenome assembled genomes (MAGs) from these data and others will further our understanding of the ecology and evolution of hot spring anoxygenic phototrophs. IMPORTANCE Photosynthetic bacteria in hot springs are of great importance to both microbial evolution and ecology. While a large body of work has focused on oxygenic photosynthesis in cyanobacteria in Mushroom and Octopus Springs in Yellowstone National Park, many questions remain regarding the metabolic potential and ecology of hot spring anoxygenic phototrophs. Anoxygenic phototrophs are metabolically and taxonomically diverse, and further investigations into their physiology will lead to a deeper understanding of microbial evolution and ecology of these taxa. Here, we have quantified the distribution of key genes involved in carbon and nitrogen metabolism in both oxygenic and anoxygenic phototrophs. Our results suggest that temperature >68ºC selects for distinct groups of cyanobacteria and that carbon fixation pathways associated with these taxa are likely subject to the same selective pressure. Additionally, our data suggest that phototrophic Chloroflexi genes and carbon fixation genes are largely influenced by local conditions as evidenced by our gene variant analysis. Lastly, we recovered several genes associated with potentially novel phototrophic Chloroflexi. Together, our results add to the body of work on hot springs in Yellowstone National Park and set the stage for future work on metagenome assembled genomes.

Biosynthetic potential of the global ocean microbiome

Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups¹, this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds^2,3. However, studying this diversity to identify genomic pathways for the synthesis of such compounds⁴ and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters (‘Candidatus Eudoremicrobiaceae’) that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments.

Global ocean microbiome survey reveals the bacterial family ‘Candidatus Eudoremicrobiaceae’, which includes some of the most biosynthetically diverse microorganisms in the ocean environment.

Bacterial microbiomes from mucus and breath of southern resident killer whales (Orcinus orca)

Opportunities to assess odontocete health are restricted due to their limited time at the surface, relatively quick movements and large geographic ranges. For endangered populations such as the southern resident killer whales (SKRWs) of the northeast Pacific Ocean, taking advantage of non-invasive samples such as expelled mucus and exhaled breath is appealing. Over the past 12 years, such samples were collected, providing a chance to analyse and assess their bacterial microbiomes using amplicon sequencing. Based on operational taxonomic units, microbiome communities from SRKW and transient killer whales showed little overlap between mucus, breath and seawater from SRKW habitats and six bacterial phyla were prominent in expelled mucus but not in seawater. Mollicutes and Fusobacteria were common and abundant in mucus, but not in breath or seawater, suggesting these bacterial classes may be normal constituents of the SRKW microbiome. Out of 134 bacterial families detected, 24 were unique to breath and mucus, including higher abundances of Burkholderiaceae, Moraxellaceae and Chitinophagaceae. Although there were multiple bacterial genera in breath or mucus that include pathogenic species (e.g. Campylobacter, Hemophilus, Treponema), the presence of these bacteria is not necessarily evidence of disease or infection. Future emphasis on genotyping mucus samples to the individual animal will allow further assessment in the context of that animal's history, including body condition index and prior contaminants burden. This study is the first to examine expelled mucus from cetaceans for microbiomes and demonstrates the value of analysing these types of non-invasive samples.

Geobacter sp. Strain IAE Dihaloeliminates 1,1,2-Trichloroethane and 1,2-Dichloroethane

Chlorinated ethanes, including 1,2-dichloroethane (1,2-DCA) and 1,1,2-trichloroethane (1,1,2-TCA), are widespread groundwater contaminants. Enrichment cultures XR_DCA and XR_TCA derived from river sediment dihaloeliminated 1,2-DCA to ethene and 1,1,2-TCA to vinyl chloride (VC), respectively. The XR_TCA culture subsequently converted VC to ethene via hydrogenolysis. Microbial community profiling demonstrated the enrichment of Geobacter 16S rRNA gene sequences in both the XR_DCA and XR_TCA cultures, and Dehalococcoides mccartyi (Dhc) sequences were only detected in the ethene-producing XR_TCA culture. The presence of a novel Geobacter population, designated as Geobacter sp. strain IAE, was identified by the 16S rRNA gene-targeted polymerase chain reaction and Sanger sequencing. Time-resolved population dynamics attributed the dihaloelimination activity to strain IAE, which attained the growth yields of 0.93 ± 0.06 × 10⁷ and 1.18 ± 0.14 × 10⁷ cells per μmol Cl^- released with 1,2-DCA and 1,1,2-TCA as electron acceptors, respectively. In contrast, Dhc growth only occurred during VC-to-ethene hydrogenolysis. Our findings discover a Geobacter sp. strain capable of respiring multiple chlorinated ethanes and demonstrate the involvement of a broader diversity of organohalide-respiring bacteria in the detoxification of 1,2-DCA and 1,1,2-TCA.

Characterization of the First Cultured Representative of "Candidatus Thermofonsia" Clade 2 within Chloroflexi Reveals Its Phototrophic Lifestyle

“Candidatus Thermofonsia” represents a novel class within the phylum Chloroflexi. Metagenomic analysis reveals “Ca. Thermofonsia” harbors phototrophs outside the classically phototrophic Chloroflexia class. Unfortunately, the paucity of pure cultures limits further insights into their potential phototrophy. Here, we report the successful isolation of a “Ca. Thermofonsia” representative (Phototrophicus methaneseepsis ZRK33) from a deep-sea cold seep. Using combined physiological, genomic, and transcriptomic methods, we further show the long-wavelength light (e.g., red and infrared light) could promote the growth of strain ZRK33 and upregulate the expression of genes associated with phototrophy. In particular, strain ZRK33 has a typical phototrophic lifestyle under both laboratory and deep-sea conditions. Strain ZRK33 also possesses the ability to fix inorganic carbon through the 3-hydroxypropionate bicycle in both laboratory and deep-sea in situ environments, and the combined autotrophic, phototrophic, and heterotrophic capabilities endow strain ZRK33 with a photomixotrophic lifestyle. Notably, the predicted genes associated with phototrophy broadly exist in the metagenomes of 27 deep-sea Chloroflexi members, strongly suggesting diverse phototrophic Chloroflexi members are distributed in various unexplored deep biospheres.

Out of Thin Air? Astrobiology and Atmospheric Chemotrophy

The emerging understanding of microbial trace gas chemotrophy as a metabolic strategy to support energy and carbon acquisition for microbial survival and growth has significant implications in the search for past, and even extant, life beyond Earth. The use of trace gases, including hydrogen and carbon monoxide as substrates for microbial oxidation, potentially offers a viable strategy with which to support life on planetary bodies that possess a suitable atmospheric composition, such as Mars and Titan. Here, we discuss the current state of knowledge of this process and explore its potential in the field of astrobiological exploration.

Endolithic Bacterial Diversity in Lichen-Dominated Communities Is Shaped by Sun Exposure in McMurdo Dry Valleys, Antarctica

The diversity and composition of endolithic bacterial diversity of several locations in McMurdo Dry Valleys (Continental Antarctica) were explored using amplicon sequencing, targeting the V3 and V4 of the 16S region. Despite the increasing interest in edaphic factors that drive bacterial community composition in Antarctic rocky communities, few researchers focused attention on the direct effects of sun exposure on bacterial diversity; we herein reported significant differences in the northern and southern communities. The analysis of β-diversity showed significant differences among sampled localities. For instance, the most abundant genera found in the north-exposed rocks were Rhodococcus and Blastococcus in Knobhead Mt.; Ktedonobacter and Cyanobacteria Family I Group I in Finger Mt.; Rhodococcus and Endobacter in University Valley; and Segetibacter and Tetrasphaera in Siegfried Peak samples. In south-exposed rocks, instead, the most abundant genera were Escherichia/Shigella and Streptococcus in Knobhead Mt.; Ktedonobacter and Rhodococcus in Finger Mt.; Ktedonobacter and Roseomonas in University Valley; and Blastocatella, Cyanobacteria Family I Group I and Segetibacter in Siegfried Peak. Significant biomarkers, detected by the Linear discriminant analysis Effect Size, were also found among north- and south-exposed communities. Besides, the large number of positive significant co-occurrences may suggest a crucial role of positive associations over competitions under the harsher conditions where these rock-inhabiting microorganisms spread. Although the effect of geographic distances in these extreme environments play a significant role in shaping biodiversity, the study of an edaphic factor, such as solar exposure, adds an important contribution to the mosaic of microbial biodiversity of Antarctic bacterial cryptoendolithic communities.

Phylum Gemmatimonadota and Its Role in the Environment

Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.

Microbial community structures and important taxa across oxygen gradients in the Andaman Sea and eastern Bay of Bengal epipelagic waters

In oceanic oxygen minimum zones (OMZs), the abundances of aerobic organisms significantly decrease and energy shifts from higher trophic levels to microorganisms, while the microbial communities become critical drivers of marine biogeochemical cycling activities. However, little is known of the microbial ecology of the Andaman Sea and eastern Bay of Bengal (BoB) OMZs. In the present study, a total of 131 samples which from the Andaman Sea and eastern BoB epipelagic waters were analyzed. The microbial community distribution patterns across oxygen gradients, including oxygenic zones (OZs, dissolved oxygen [DO] ≥ 2 mg/L), oxygen limited zones (OLZs, 0.7 mg/L < DO < 2 mg/L), and OMZs (DO ≤ 0.7 mg/L), were investigated. Mantel tests and Spearman's correlation analysis revealed that DO was the most important driver of microbial community structures among several environmental factors. Microbial diversity, richness, and evenness were highest in the OLZs and lowest in the OZs. The microbial community compositions of OZ and OMZ waters were significantly different. Random forest analysis revealed 24 bioindicator taxa that differentiated OZ, OLZ, and OMZ water communities. These bioindicator taxa included Burkholderiaceae, HOC36, SAR11 Clade IV, Thioglobaceae, Nitrospinaceae, SAR86, and UBA10353. Further, co-occurrence network analysis revealed that SAR202, AEGEAN-169, UBA10353, SAR406, and Rhodobacteraceae were keystone taxa among the entire interaction network of the microbial communities. Functional prediction further indicated that the relative abundances of microbial populations involved in nitrogen and sulfur cycling were higher in OMZs. Several microbial taxa, including the Thioglobaceae, Nitrospinaceae, SAR202, SAR406, WPS-2, UBA10353, and Woeseiaceae, may be involved in nitrogen and/or sulfur cycling, while also contributing to oxygen consumption in these waters. This study consequently provides new insights into the microbial community structures and potentially important taxa that contribute to oxygen consumption in the Andaman Sea and eastern BoB OMZ.

Efficient removal of organic compounds from shale gas wastewater by coupled ozonation and moving-bed-biofilm submerged membrane bioreactor

Shale gas wastewater (SGW) with complex composition and high salinity needs an economical and efficient method of treatment with the main goal to remove organics. In this study, a coupled system consisting of ozonation and moving-bed-biofilm submerged membrane bioreactor (MBBF-SMBR) was comprehensively evaluated for SGW treatment and compared with a similar train comprising ozonation and submerged membrane bioreactor (SMBR) without addition of carriers attaching biofilm. The average removal rates of MBBF-SMBR were 77.8% for dissolved organic carbon (DOC) and 37.0% for total nitrogen (TN), higher than those observed in SMBR, namely, 73.9% for DOC and 18.6% for TN. The final total membrane resistance in SMBR was 40.1% higher than that in MBBF-SMBR. Some genera that specifically contribute to organic removal were identified. Enhanced gene allocation for membrane transport and nitrogen metabolism was found in MBBF-SMBR biofilm, implying that this system has significant industrial application potential for organics removal from SGW.

Succession of Microbial Communities in Waste Soils of an Iron Mine in Eastern China

The reclamation of mine dump is largely centered on the role played by microorganisms. However, the succession of microbial community structure and function in ecological restoration of the mine soils is still poorly understood. In this study, soil samples with different stacking time were collected from the dump of an iron mine in China and the physicochemical characteristics and microbial communities of these samples were comparatively investigated. The results showed that the fresh bare samples had the lowest pH, highest ion concentration, and were the most deficient in nutrients while the acidity and ion concentration of old bare samples decreased significantly, and the nutritional conditions improved remarkably. Vegetated samples had the weakest acidity, lowest ion concentration, and the highest nutrient concentration. In the fresh mine soils, the iron/sulfur-oxidizers such as Acidiferrobacter and Sulfobacillus were dominant, resulting in the strongest acidity. Bacteria from genera Acidibacter, Metallibacterium, and phyla Cyanobacteria, WPS-2 were abundant in the old bare samples, which contributed to the pH increase and TOC accumulation respectively. Acidobacteriota predominated in the vegetated samples and promoted nutrient enrichment and plant growth significantly. The microbial diversity and evenness of the three types of soils increased gradually, with more complex microbial networks, suggesting that the microbial community became more mature with time and microorganisms co-evolved with the mine soils.

Impact assessment of ephemeral discharge of contamination downstream of two legacy base metal mines using environmental DNA

Mining and processing metalliferous ores can degrade the environment well beyond the footprint of the mine, particularly where on-site containment and post-mining remediation has been insufficient to prevent releases of solid and aqueous mine wastes. In this study, we investigated the potential of sediment and water chemistry coupled with environmental (e)DNA metabarcoding to evaluate discrete and cumulative ecological impacts of two legacy base metal (copper (Cu), zinc (Zn), lead (Pb)) mines (Peelwood and Cordillera) which discharge metals via ephemeral tributaries into perennial Peelwood Creek. Although the two mine streams exceeded Australian guidelines for sediment and freshwater quality for Cu, Zn and Pb, Peelwood Creek had relatively low sediment and water metal concentrations, suggesting a low potential for environmental toxicity. Although sediment and water chemistry defined the extent of biological impacts, metabarcoding showed that Peelwood and Cordillera mines had discrete impacts and Peelwood mine was the main source of contamination of Peelwood Creek. Metabarcoding showed that prokaryotes can be good indicators of metal contamination whereas eukaryotes did not reflect contamination impacts in Peelwood Creek. Metabarcoding results showed that benthic communities downstream of Cordillera mine were less impacted than those below Peelwood mine, suggesting that Peelwood mine should be considered for further remediation.

Exploitation of extracellular organic matter from Micrococcus luteus to enhance ex situ bioremediation of soils polluted with used lubricants

Chronic pollution by used lubricant oils (ULOs) poses a serious challenge to the environment. Under stress conditions, microorganisms, including potential degraders, can enter a viable but non-culturable (VBNC) state, complicating the bioremediation of ULO-polluted areas. Resuscitation-promoting factors (Rpfs) can reverse this transition and/or enhance the biodegradation performance of both native and augmented strains. Here, Rpf-containing extracellular organic matter (EOM) from Micrococcus luteus was used to enhance the ex situ ULO removal in biostimulated and bioaugmented (with Rhodococcus qingshengii KAG C, R. erythropolis PR4) soils. ULO bioconversion, microbial activity, and CFUs were significantly higher in EOM-treated soils compared to corresponding control soils. After 60 days, the initial ULO concentration (52,500 mg kg^-1) was reduced by 37% and 45% with EOM-supplemented biostimulation and bioaugmentation, respectively. Based on high-throughput 16S rRNA analysis, the enhancement was attributable both to the reactivation of EOM-responsive hydrocarbonoclastic bacterial genera (e.g., Pseudomonas, Comamonas, Stenotrophomonas, Gordonia) and to the long-term positive effect of EOM on the degradative efficacy of the introduced rhodococci. Ecotoxicological responses revealed that reduced ULO concentration did not correlate with decreased soil toxicity. Our findings provide an insight into the applicability of EOM in bioremediation and its effects on the soil microbial activity and community composition.

Complex History of Aerobic Respiration and Phototrophy in the Chloroflexota Class Anaerolineae Revealed by High-Quality Draft Genome of Ca. Roseilinea mizusawaensis AA3_104

Roseilinea is a novel lineage of Chloroflexota known only from incomplete metagenome-assembled genomes (MAGs) and preliminary enrichments. Roseilinea is notable for appearing capable of anoxygenic photoheterotrophy despite being only distantly related to well-known phototrophs in the Chloroflexia class such as Chloroflexus and Roseiflexus. Here, we present a high-quality MAG of a member of Roseilinea, improving our understanding of the metabolic capacity and phylogeny of this genus, and resolving the multiple instances of horizontal gene transfer that have led to its metabolic potential. These data allow us to propose a candidate family for these organisms, Roseilineaceae, within the Anaerolineae class.

Recent advances in the structural diversity of reaction centers

Photosynthetic reaction centers (RC) catalyze the conversion of light to chemical energy that supports life on Earth, but they exhibit substantial diversity among different phyla. This is exemplified in a recent structure of the RC from an anoxygenic green sulfur bacterium (GsbRC) which has characteristics that may challenge the canonical view of RC classification. The GsbRC structure is analyzed and compared with other RCs, and the observations reveal important but unstudied research directions that are vital for disentangling RC evolution and diversity. Namely, (1) common themes of electron donation implicate a Ca2+ site whose role is unknown; (2) a previously unidentified lipid molecule with unclear functional significance is involved in the axial ligation of a cofactor in the electron transfer chain; (3) the GsbRC features surprising structural similarities with the distantly-related photosystem II; and (4) a structural basis for energy quenching in the GsbRC can be gleaned that exemplifies the importance of how exposure to oxygen has shaped the evolution of RCs. The analysis highlights these novel avenues of research that are critical for revealing evolutionary relationships that underpin the great diversity observed in extant RCs.

Candidatus Eremiobacterota, a metabolically and phylogenetically diverse terrestrial phylum with acid-tolerant adaptations

Candidatus phylum Eremiobacterota (formerly WPS-2) is an as-yet-uncultured bacterial clade that takes its name from Ca. Eremiobacter, an Antarctic soil aerobe proposed to be capable of a novel form of chemolithoautotrophy termed atmospheric chemosynthesis, that uses the energy derived from atmospheric H₂-oxidation to fix CO₂ through the Calvin-Benson-Bassham (CBB) cycle via type 1E RuBisCO. To elucidate the phylogenetic affiliation and metabolic capacities of Ca. Eremiobacterota, we analysed 63 public metagenome-assembled genomes (MAGs) and nine new MAGs generated from Antarctic soil metagenomes. These MAGs represent both recognized classes within Ca. Eremiobacterota, namely Ca. Eremiobacteria and UBP9. Ca. Eremiobacteria are inferred to be facultatively acidophilic with a preference for peptides and amino acids as nutrient sources. Epifluorescence microscopy revealed Ca. Eremiobacteria cells from Antarctica desert soil to be coccoid in shape. Two orders are recognized within class Ca. Eremiobacteria: Ca. Eremiobacterales and Ca. Baltobacterales. The latter are metabolically versatile, with individual members having genes required for trace gas driven autotrophy, anoxygenic photosynthesis, CO oxidation, and anaerobic respiration. UBP9, here renamed Ca. Xenobia class. nov., are inferred to be obligate heterotrophs with acidophilic adaptations, but individual members having highly divergent metabolic capacities compared to Ca. Eremiobacteria, especially with regard to respiration and central carbon metabolism. We conclude Ca. Eremiobacterota to be an ecologically versatile phylum with the potential to thrive under an array of "extreme" environmental conditions.

Characterizing the Uncultivated Microbial Minority: towards Understanding the Roles of the Rare Biosphere in Microbial Communities

Microbial communities are frequently numerically dominated by just a few species. Often, the long “tail” of the rank-abundance plots of microbial communities constitutes the so-called “rare biosphere,” microorganisms that are highly diverse but are typically found in low abundance in these communities. Their presence in microbial communities has only recently become apparent with advances in high-throughput sequencing technologies. Despite their low numbers, they are thought to play important roles in their communities and may function as potential members to keep the communities intact and resilient. Their phylogenetic diversity also means that they are important subjects for better understanding the interplay between microbial diversity and evolution. I propose that more efforts should be put into characterizing these poorly understood and mostly unknown microbial lineages that hold vast potentials for our understanding of microbial diversity, ecology, and evolution of life on this planet.

Application of environmental DNA for assessment of contamination downstream of a legacy base metal mine

Acid Rock Drainage (ARD) from legacy mines can negatively impact the biota in sediments and waters for tens of kilometers downstream. Here we used environmental (e)DNA metabarcoding to assess the impacts of metal contaminants on biota in sediment and water downstream of a legacy base metal sulfide mine in southeastern Australia, as exemplar of similar mines elsewhere. Concentrations of metals in water were below Australian water quality guideline values at 20 km downstream for copper (Cu), 40 km downstream for zinc (Zn) and 10 km downstream for lead (Pb). Sediment metal concentrations were below national guideline concentrations at 10 km downstream for Cu, 60 km downstream for Zn and 20 km downstream for Pb. In contrast, metabarcoding showed that biological communities from sediment samples at 10 km and 20 km downstream were similar to sites close to the mine and thus indicative of being impacted, despite metal concentrations being relatively low. As we illustrate, when combined with sediment and water chemistry, metabarcoding can provide more ecological robust perspective on the downstream effects of legacy mines, capturing the sensitivities of a diverse range of organisms.

Time-resolved comparative molecular evolution of oxygenic photosynthesis

Oxygenic photosynthesis starts with the oxidation of water to O2, a light-driven reaction catalysed by photosystem II. Cyanobacteria are the only prokaryotes capable of water oxidation and therefore, it is assumed that the origin of oxygenic photosynthesis is a late innovation relative to the origin of life and bioenergetics. However, when exactly water oxidation originated remains an unanswered question. Here we use phylogenetic analysis to study a gene duplication event that is unique to photosystem II: the duplication that led to the evolution of the core antenna subunits CP43 and CP47. We compare the changes in the rates of evolution of this duplication with those of some of the oldest well-described events in the history of life: namely, the duplication leading to the Alpha and Beta subunits of the catalytic head of ATP synthase, and the divergence of archaeal and bacterial RNA polymerases and ribosomes. We also compare it with more recent events such as the duplication of Cyanobacteria-specific FtsH metalloprotease subunits and the radiation leading to Margulisbacteria, Sericytochromatia, Vampirovibrionia, and other clades containing anoxygenic phototrophs. We demonstrate that the ancestral core duplication of photosystem II exhibits patterns in the rates of protein evolution through geological time that are nearly identical to those of the ATP synthase, RNA polymerase, or the ribosome. Furthermore, we use ancestral sequence reconstruction in combination with comparative structural biology of photosystem subunits, to provide additional evidence supporting the premise that water oxidation had originated before the ancestral core duplications. Our work suggests that photosynthetic water oxidation originated closer to the origin of life and bioenergetics than can be documented based on phylogenetic or phylogenomic species trees alone.

Enhancement of nitrite-dependent anaerobic methane oxidation via Geobacter sulfurreducens

Nitrite-dependent anaerobic methane-oxidation (n-damo) is a potential novel technology for nitrogen removal in anaerobic wastewater treatment. In this study, Geobacter sulfurreducens (G) was applied to stimulate n-damo activity. Conductive materials such as nano-magnetite (M) or aggregating agents such as hydroxylapatite (H) were co-added with G. sulfurreducens to further investigate the enhancement effect. Results showed that the nitrite reduction activity of the n-damo culture was promoted by G. sulfurreducens, with 1.71-2.38 times higher in treatment G, G + M, and G + H than that in the control, but was inhibited by the single addition of hydroxylapatite. N-damo bacterial abundances based on the qPCR of the n-damo-specific pmoA gene increased in treatments with G. sulfurreducens, compared with that of the control. High-throughput sequencing analysis revealed the enrichment of uncultured phylum WPS-2 in treatments with G. sulfurreducens. Fluorescence in situ hybridization verified the co-occurrence pattern of n-damo bacteria (NC10), G. sulfurreducens, and type-I aerobic methanotrophs (Methylomonas spp.). The above results corroborated the microbial interspecies electron transfer (MIET) potentiality of the n-damo enrichment. Our study provides a novel pathway for enhancing MIET to stimulate n-damo process.

Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps)

The warming-induced thawing of permafrost promotes microbial activity, often resulting in enhanced greenhouse gas emissions. The ability of permafrost microorganisms to survive the in situ sub-zero temperatures, their energetic strategies and their metabolic versatility in using soil organic materials determine their growth and functionality upon thawing. Hence, functional characterization of the permafrost microbiome, particularly in the underexplored mid-latitudinal alpine regions, is a crucial first step in predicting its responses to the changing climate, and the consequences for soil-climate feedbacks. In this study, for the first time, the functional potential and metabolic capabilities of a temperate mountain permafrost microbiome from central Europe has been analysed using shotgun metagenomics. Permafrost and active layers from the summit of Muot da Barba Peider (MBP) [Swiss Alps, 2979 m above sea level (a.s.l.)] revealed a strikingly high functional diversity in the permafrost (north-facing soils at a depth of 160 cm). Permafrost metagenomes were enriched in stress-response genes (e.g. cold-shock genes, chaperones), as well as in genes involved in cell defence and competition (e.g. antiviral proteins, antibiotics, motility, nutrient-uptake ABC transporters), compared with active-layer metagenomes. Permafrost also showed a higher potential for the synthesis of carbohydrate-active enzymes, and an overrepresentation of genes involved in fermentation, carbon fixation, denitrification and nitrogen reduction reactions. Collectively, these findings demonstrate the potential capabilities of permafrost microorganisms to thrive in cold and oligotrophic conditions, and highlight their metabolic versatility in carbon and nitrogen cycling. Our study provides a first insight into the high functional gene diversity of the central European mountain permafrost microbiome. Our findings extend our understanding of the microbial ecology of permafrost and represent a baseline for future investigations comparing the functional profiles of permafrost microbial communities at different latitudes.

Candidatus Anthektikosiphon siderophilum OHK22, a New Member of the Chloroflexi Family Herpetosiphonaceae from Oku-okuhachikurou Onsen

We report the draft metagenome-assembled genome of a member of the Chloroflexi family Herpetosiphonaceae from microbial biofilms developed in a circumneutral, iron-rich hot spring in Japan. This taxon represents a novel genus and species—here proposed as Candidatus Anthektikosiphon siderophilum—that expands the known taxonomic and genetic diversity of the Herpetosiphonaceae and helps orient the evolutionary history of key traits like photosynthesis and aerobic respiration in the Chloroflexi.

Common Presence of Phototrophic Gemmatimonadota in Temperate Freshwater Lakes

Members of the bacterial phylum Gemmatimonadota are ubiquitous in most natural environments and represent one of the top 10 most abundant bacterial phyla in soil. Sequences affiliated with Gemmatimonadota were also reported from diverse aquatic habitats; however, it remains unknown whether they are native organisms or represent bacteria passively transported from sediment or soil. To address this question, we analyzed metagenomes constructed from five freshwater lakes in central Europe. Based on the 16S rRNA gene frequency, Gemmatimonadota represented from 0.02 to 0.6% of all bacteria in the epilimnion and between 0.1 and 1% in the hypolimnion. These proportions were independently confirmed using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Some cells in the epilimnion were attached to diatoms (Fragilaria sp.) or cyanobacteria (Microcystis sp.), which suggests a close association with phytoplankton. In addition, we reconstructed 45 metagenome-assembled genomes (MAGs) related to Gemmatimonadota They represent several novel lineages, which persist in the studied lakes during the seasons. Three lineages contained photosynthesis gene clusters. One of these lineages was related to Gemmatimonas phototrophica and represented the majority of Gemmatimonadota retrieved from the lakes' epilimnion. The other two lineages came from hypolimnion and probably represented novel photoheterotrophic genera. None of these phototrophic MAGs contained genes for carbon fixation. Since most of the identified MAGs were present during the whole year and cells associated with phytoplankton were observed, we conclude that they represent truly limnic Gemmatimonadota distinct from the previously described species isolated from soils or sediments.IMPORTANCE Photoheterotrophic bacterial phyla such as Gemmatimonadota are key components of many natural environments. Its first photoheterotrophic cultured member, Gemmatimonas phototrophica, was isolated in 2014 from a shallow lake in the Gobi Desert. It contains a unique type of photosynthetic complex encoded by a set of genes which were likely received via horizontal transfer from Proteobacteria We were intrigued to discover how widespread this group is in the natural environment. In the presented study, we analyzed 45 metagenome-assembled genomes (MAGs) that were obtained from five freshwater lakes in Switzerland and Czechia. Interestingly, it was found that phototrophic Gemmatimonadota are relatively common in euphotic zones of the studied lakes, whereas heterotrophic Gemmatimonadota prevail in deeper waters. Moreover, our analysis of the MAGs documented that these freshwater species contain almost the same set of photosynthesis genes identified before in Gemmatimonas phototrophica originating from the Gobi Desert.

Granick revisited: Synthesizing evolutionary and ecological evidence for the late origin of bacteriochlorophyll via ghost lineages and horizontal gene transfer

Photosynthesis-both oxygenic and more ancient anoxygenic forms-has fueled the bulk of primary productivity on Earth since it first evolved more than 3.4 billion years ago. However, the early evolutionary history of photosynthesis has been challenging to interpret due to the sparse, scattered distribution of metabolic pathways associated with photosynthesis, long timescales of evolution, and poor sampling of the true environmental diversity of photosynthetic bacteria. Here, we reconsider longstanding hypotheses for the evolutionary history of phototrophy by leveraging recent advances in metagenomic sequencing and phylogenetics to analyze relationships among phototrophic organisms and components of their photosynthesis pathways, including reaction centers and individual proteins and complexes involved in the multi-step synthesis of (bacterio)-chlorophyll pigments. We demonstrate that components of the photosynthetic apparatus have undergone extensive, independent histories of horizontal gene transfer. This suggests an evolutionary mode by which modular components of phototrophy are exchanged between diverse taxa in a piecemeal process that has led to biochemical innovation. We hypothesize that the evolution of extant anoxygenic photosynthetic bacteria has been spurred by ecological competition and restricted niches following the evolution of oxygenic Cyanobacteria and the accumulation of O2 in the atmosphere, leading to the relatively late evolution of bacteriochlorophyll pigments and the radiation of diverse crown group anoxygenic phototrophs. This hypothesis expands on the classic "Granick hypothesis" for the stepwise evolution of biochemical pathways, synthesizing recent expansion in our understanding of the diversity of phototrophic organisms as well as their evolving ecological context through Earth history.

Deciphering the rhizosphere microbiome of a bamboo plant in response to different chromium contamination levels

Bamboo has been considered a potential plant species for phytoremediation due to its high biomass and heavy metal (HM) resistance. However, little is known about the interactions between bamboo and soil microbial activities in HM-contaminated soils. Here, we investigated the characteristics of microbial communities in the rhizosphere soil of Lei bamboo (Phyllostachys praecox) along a chromium (Cr) gradient. We found that the soil Cr content was positively correlated with the total organic carbon (TOC) and HCl-extractable Cr but negatively correlated with the pH and bacterial and fungal Shannon indices. Proteobacteria and Ascomycota predominated in the bamboo rhizosphere under Cr pollution. A co-occurrence network showed that two of the most Cr-sensitive bacterial genera and keystone taxa were from the Acidobacteria, indicating that this phylum can be as an indicator for the studied Cr-polluted soils. Redundancy analysis revealed that both the soil bacterial and fungal community compositions were significantly correlated (p < 0.05) with Cr, pH, TOC, alkali-hydrolysable N (AN), and available phosphorus (AP). The increase in TOC as the Cr content increased can be ascribed to an adverse Cr effect on the soil microflora, probably because the microbial biomass was less effective in mineralizing soil C under Cr-polluted conditions.

Temperature impacts community structure and function of phototrophic Chloroflexi and Cyanobacteria in two alkaline hot springs in Yellowstone National Park

Photosynthetic bacteria are abundant in alkaline, terrestrial hot springs and there is a long history of research on phototrophs in Yellowstone National Park (YNP). Hot springs provide a framework to examine the ecophysiology of phototrophs in situ because they provide natural gradients of geochemistry, pH and temperature. Phototrophs within the Cyanobacteria and Chloroflexi groups are frequently observed in alkaline hot springs. Decades of research has determined that temperature constrains Cyanobacteria in alkaline hot springs, but factors that constrain the distribution of phototrophic Chloroflexi remain unresolved. Using a combination of 16S rRNA gene sequencing and photoassimilation microcosms, we tested the hypothesis that temperature would constrain the activity and composition of phototrophic Cyanobacteria and Chloroflexi. We expected diversity and rates of photoassimilation to decrease with increasing temperature. We report 16S rRNA amplicon sequencing along with carbon isotope signatures and photoassimilation from 45 to 72°C in two alkaline hot springs. We find that Roseiflexus, Chloroflexus (Chloroflexi) and Leptococcus (Cyanobacteria) operational taxonomic units (OTUs) have distinct distributions with temperature. This distribution suggests that, like phototrophic Cyanobacteria, temperature selects for specific phototrophic Chloroflexi taxa. The richness of phototrophic Cyanobacteria decreased with increasing temperature along with a decrease in oxygenic photosynthesis, whereas Chloroflexi richness and rates of anoxygenic photosynthesis did not decrease with increasing temperature, even at temperatures approaching the upper limit of photosynthesis (~72-73°C). Our carbon isotopic data suggest an increasing prevalence of the 3-hydroxypropionate pathway with decreasing temperature coincident with photoautotrophic Chloroflexi. Together these results indicate temperature plays a role in defining the niche space of phototrophic Chloroflexi (as has been observed for Cyanobacteria), but other factors such as morphology, geochemistry, or metabolic diversity of Chloroflexi, in addition to temperature, could determine the niche space of this highly versatile group.