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

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

Testing the ectomycorrhizal-dominance hypothesis for ecosystem multifunctionality in a subtropical mountain forest.

Mycorrhizal associations are key mutualisms that shape the structure of forest communities and multiple ecosystem functions. However, we lack a framework for predicting the varying dominance of distinct mycorrhizal associations in an integrated proxy of multifunctionality across ecosystems. Here, we used the datasets containing diversity of mycorrhizal associations and 18 ecosystem processes related to supporting, provisioning, and regulating services to examine how the dominance of ectomycorrhiza (EcM) associations affects ecosystem multifunctionality in subtropical mountain forests in Southwest China. Meanwhile, we synthesized the prevalence of EcM-dominant effects on ecosystem functioning in forest biomes. Our results demonstrated that elevation significantly modified the distributions of EcM trees and fungal dominance, which in turn influenced multiple functions simultaneously. Multifunctionality increased with increasing proportion of EcM associations, supporting the ectomycorrhizal-dominance hypothesis. Meanwhile, we observed that the impacts of EcM dominance on individual ecosystem functions exhibited different relationships among forest biomes. Our findings highlight the importance of ectomycorrhizal dominance in regulating multifunctionality in subtropical forests. However, this ectomycorrhizal feedback in shaping ecosystem functions cannot necessarily be generalized across forests. Therefore, we argue that the predictions for ecosystem multifunctionality in response to the shifts of mycorrhizal composition could vary across space and time.

Temporal variation of microbial nutrient limitation in citrus plantations: Insights from soil enzyme stoichiometry.

Soil enzyme carbon (C): nitrogen (N): phosphorous (P) stoichiometry and their vector model has been widely used to elucidate the balance between microbial nutrient requirements and soil nutrient availability. However, limited knowledge is available on the dynamics of soil enzyme stoichiometry and microbial nutrient limitation following afforestation, especially in the economic forest. In this study, the effects of citrus plantation on C: N: P stoichiometry were assessed through a comparative study between cropland and citrus plantations with varying durations of afforestation (i.e., 3, 15, 25, and 35 years). It was found that the C, N, and P contents in the soil (SOC, STN, and STP), microbial biomass (MBC, MBN, and MBP), as well as the activities of C-, N-, and P-acquiring enzymes (BG, NAG, and AP), were 1.02-2.51 times higher than those in cropland. Additionally, C, N, and P contents in soil and microbial biomass increased consistently with increasing afforestation time. While the activities of C-, N-, and P-acquiring enzymes increased from 3 years to 25 years and then significantly decreased. In addition to NAG: AP, the stoichiometry of C, N, and P in soil (SOC: STN, SOC: STP, and STN: STP) and microbial biomass (MBC: MBN, MBC: MBP, and MBN: MBP), along with BG: NAG, exhibited a decline of 7.69-27.38% compared to cropland. Moreover, the majority of the C: N: P stoichiometry in soil, microbial biomass, and enzymes consistently decreased with increasing afforestation time, except for SOC: STN and NAG: AP, which exhibited an opposite trend. Furthermore, a significant decrease in microbial carbon limitation and an increase in microbial nitrogen limitation were observed with increasing afforestation time. Collectively, the dynamic of microbial nutrient limitation was primarily influenced by the interaction between soil nutrients and edaphic factors. The findings suggest that with the increasing duration of citrus plantation, it is crucial to focus on nitrogen (N) fertilization while maintaining a delicate balance between fertilization strategies and soil acidity levels.

Habitat- and lifestyle-dependent structural and functional characteristics of viruses in mangrove wetlands of different functional zonings.

Mangrove wetlands, as one of the natural ecosystems with the most ecological services, have garnered widespread attention about their microbial driven biogeochemical cycling. Urbanization have led to different spatial patterns of environmental conditions and microbial communities in mangroves. However, viruses, as the pivotal drivers of biogeochemical cycling in mangroves, remain inadequately explored in terms of how their ecological potential and complex interactions with host respond to functional zonings. To address this knowledge gap, we conducted a comprehensive investigation on the structural and functional properties of temperate and lytic viruses in mangrove wetlands from different functional zonings by jointly using high-throughput sequencing, prokaryotic and viral metagenomics. Multiple environmental factors were found to significantly influence the taxonomic and functional composition, as well as lysogen-lysis decision-making of mangrove viruses. Furthermore, enriched auxiliary metabolic genes (AMGs) involved in methane, nitrogen and sulfur metabolism, and heavy metal resistance were unveiled in mangrove viruses, whose community composition was closely related to lifestyle and host. The virus-host pairs with different lifestyles were also discovered to react to environmental changes in different ways, which provided an empirical evidence for how virus and bacteria dynamics were specific to viral lifestyles in nature. This study expands our comprehension of the intricate interactions among virus, prokaryotic host and the environment in mangrove wetlands from multiple perspectives, including viral lifestyles, virus-host interactions, and habitat dependence. Importantly, it provides a new ecological perspective on how mangrove viruses are adapted to the stress posed by urbanization.

Mulches assist degraded soil recovery via stimulating biogeochemical cycling: metagenomic analysis.

Soil degradation of urban greening has caused soil fertility loss and soil organic carbon depletion. Organic mulches are made from natural origin materials, and represent a cost-effective and environment-friendly remediation method for urban greening. To reveal the effects of organic mulch on soil physicochemical characteristics and fertility, we selected a site that was covered with organic mulch for 6 years and a nearby lawn-covered site. The results showed that soil organic matter, total nitrogen, and available phosphorus levels were improved, especially at a depth of 0-20 cm. The activities of cellulase, invertase, and dehydrogenase in soil covered with organic mulch were 17.46%, 78.98%, and 283.19% higher than those under lawn, respectively. The marker genes of fermentation, aerobic respiration, methanogenesis, and methane oxidation were also enriched in the soil under organic mulch. Nitrogen cycling was generally repressed by the organic mulch, but the assimilatory nitrate and nitrite reduction processes were enhanced. The activity of alkaline phosphatase was 12.63% higher in the mulch-covered soil, and functional genes involved in phosphorus cycling were also enriched. This study presents a comprehensive investigation of the influence of organic mulch on soil microbes and provides a deeper insight into the recovery strategy for soil degradation following urban greening. KEY POINTS: • Long-term cover with organic mulches assists soil recovery from degradation • Soil physical and chemical properties were changed by organic mulches • Organic mulches enhanced genes involved in microbially mediated C and P cycling • Soil organic matter was derived from decomposition of organic mulch and carbon fixation • N cycling was repressed by mulches, except for assimilatory NO2- and NO3- reductions.

Identification and characterization of a novel hydroxylamine oxidase, DnfA, that catalyzes the oxidation of hydroxylamine to N2.

Nitrogen (N2) gas in the atmosphere is partially replenished by microbial denitrification of ammonia. Recent study has shown that Alcaligenes ammonioxydans oxidizes ammonia to dinitrogen via a process featuring the intermediate hydroxylamine, termed "Dirammox" (direct ammonia oxidation). However, the unique biochemistry of this process remains unknown. Here, we report an enzyme involved in Dirammox that catalyzes the conversion of hydroxylamine to N2. We tested previously annotated proteins involved in redox reactions, DnfA, DnfB, and DnfC, to determine their ability to catalyze the oxidation of ammonia or hydroxylamine. Our results showed that none of these proteins bound to ammonia or catalyzed its oxidation; however, we did find DnfA bound to hydroxylamine. Further experiments demonstrated that, in the presence of NADH and FAD, DnfA catalyzed the conversion of 15N-labeled hydroxylamine to 15N2. This conversion did not happen under oxygen (O2)-free conditions. Thus, we concluded that DnfA encodes a hydroxylamine oxidase. We demonstrate that DnfA is not homologous to any known hydroxylamine oxidoreductases and contains a diiron center, which was shown to be involved in catalysis via electron paramagnetic resonance experiments. Furthermore, enzyme kinetics of DnfA were assayed, revealing a Km of 92.9 ± 3.0 µM for hydroxylamine and a kcat of 0.028 ± 0.001 s-1. Finally, we show that DnfA was localized in the cytoplasm and periplasm as well as in tubular membrane invaginations in HO-1 cells. To the best of our knowledge, we conclude that DnfA is the first enzyme discovered that catalyzes oxidation of hydroxylamine to N2.

Global analysis of the perturbation effects of metal-based nanoparticles on soil nitrogen cycling.

Although studies have investigated the effects of metal-based nanoparticles (MNPs) on soil biogeochemical processes, the results obtained thus far are highly variable. Moreover, we do not yet understand how the impact of MNPs is affected by experimental design and environmental conditions. Herein, we conducted a global analysis to synthesize the effects of MNPs on 17 variables associated with soil nitrogen (N) cycling from 62 studies. Our results showed that MNPs generally exerted inhibitory effects on N-cycling process rates, N-related enzyme activities, and microbial variables. The response of soil N cycling varied with MNP type, and exposure dose was the most decisive factor for the variations in the responses of N-cycling process rates and enzyme activities. Notably, Ag/Ag2 S and CuO had dose-dependent inhibitory effects on ammonia oxidation rates, while CuO and Zn/ZnO showed hormetic effects on nitrification and denitrification rates, respectively. Other experimental design factors (e.g., MNP size and exposure duration) also regulated the effect of MNPs on soil N cycling, and specific MNPs, such as Ag/Ag2 S, exerted stronger effects during long-term (>28 days) exposure. Environmental conditions, including soil pH, organic carbon, texture, and presence/absence of plants, significantly influenced MNP toxicity. For instance, the effects of Ag/Ag2 S on the ammonia oxidation rate and the activity of leucine aminopeptidase were more potent in acid (pH <6), organic matter-limited (organic carbon content ≤10 g kg-1 ), and coarser soils. Overall, these results provide new insights into the general mechanisms by which MNPs alter soil N processes in different environments and underscore the urgent need to perform multivariate and long-term in situ trials in simulated natural environments.

Sediment microbial community structure, enzymatic activities and functional gene abundance in the coastal hypersaline habitats.

Salt marsh vegetation, mudflat and salt production are common features in worldwide coastal areas; however, their influence on microbial community composition and structure has been poorly studied and rarely compared. In the present study, microbial community composition (phospholipid fatty acid (PLFA) profiling and 16S rRNA gene sequencing (bacterial and archaeal)) and structure, enzymatic activities and abundance of functional genes in the sediments of salt ponds (crystallizer, condenser and reservoir), mudflat and vegetated mudflat were determined. Enzyme activities (ß-glucosidase, urease and alkaline phosphatase) were considerably decreased in saltpan sediments because of elevated salinity while sediment of vegetated mudflat sediments showed the highest enzyme activities. Concentrations of total microbial biomarker PLFAs (total bacterial, Gram-positive, Gram-negative, fungal and actinomycetes) were the highest in vegetated mudflat sediments and the lowest in crystallizer sediments. Nonmetric-multidimensional scaling (NMDS) analysis of PLFA data revealed that the microbial community of crystallizer, mudflat and vegetated mudflat was significantly different from each other as well as different from condenser and reservoir. The most predominant phyla within the classified bacterial fractions were Proteobacteria followed by Firmicutes, Bacteroidetes and Planctomycetes, while Euryarchaeota and Crenarchaeota phyla dominated the classified archaeal fraction. Cyanobacterial genotypes were the most dominant in the condenser. Mudflat and vegetated mudflat supported a greater abundance of Bacteroidetes and Actinobacteria, respectively. The results of the present study suggest that salt ponds had significantly decreased the microbial and enzyme activities in comparison to mudflat and vegetated mudflat sediments due to very high salinity, ionic concentrations and devoid of vegetation. The present study expands our understanding of microbial resource utilization and adaptations of microorganisms in a hypersaline environment.

Vertical Hydrologic Exchange Flows Control Methane Emissions from Riverbed Sediments.

CH4 emissions from inland waters are highly uncertain in the current global CH4 budget, especially for streams, rivers, and other lotic systems. Previous studies have attributed the strong spatiotemporal heterogeneity of riverine CH4 to environmental factors such as sediment type, water level, temperature, or particulate organic carbon abundance through correlation analysis. However, a mechanistic understanding of the basis for such heterogeneity is lacking. Here, we combine sediment CH4 data from the Hanford reach of the Columbia River with a biogeochemical-transport model to show that vertical hydrologic exchange flows (VHEFs), driven by the difference between river stage and groundwater level, determine CH4 flux at the sediment-water interface. CH4 fluxes show a nonlinear relationship with the magnitude of VHEFs, where high VHEFs introduce O2 into riverbed sediments, which inhibit CH4 production and induce CH4 oxidation, and low VHEFs cause transient reduction in CH4 flux (relative to production) due to reduced advective CH4 transport. In addition, VHEFs lead to the hysteresis of temperature rise and CH4 emissions because high river discharge caused by snowmelt in spring leads to strong downwelling flow that offsets increasing CH4 production with temperature rise. Our findings reveal how the interplay between in-stream hydrologic flux besides fluvial-wetland connectivity and microbial metabolic pathways that compete with methanogenic pathways can produce complex patterns in CH4 production and emission in riverbed alluvial sediments.

C:N:P stoichiometry of plant-soil-microbe in the secondary succession of zokor-made mounds on Qinghai-Tibet Plateau.

The knowledge of ecological stoichiometry and stoichiometric homeostasis could contribute to exploring the balance of chemical elements in ecological recovery. However, it is largely unknown how the carbon (C), nitrogen (N), phosphorus (P), and stoichiometric characteristics in the plant-soil-microbe continuum system respond to the spontaneous secondary succession of degraded alpine grasslands. Therefore, we investigated the spontaneous secondary successional recovery of grasslands disturbed by zokor (Myospalax fontanierii) on the Qinghai-Tibetan Plateau, China, via a strategy of substituting space for time. Based on plant richness, biomass, and coverage, plant importance value was employed to assess the recovery degree of zokor-made mounds (ZMMs, large and bare patch areas constructed by zokors). Multiple statistical methods, including stoichiometric homeostatic model, network, and redundancy analysis, were conducted to decipher the stoichiometric patterns. The results indicated that plant C, C:N, and C:P increased with the recovery of ZMMs, contrary to the decrease of plant N and P. In addition, soil C, N, C:N, C:P, and N:P increased with the recovery degree, and the soil became relatively more N rich by increasing organic N under the revegetation of legumes. Meanwhile, soil microbial biomass C, N, and P increased with the recovery of ZMMs, but microbial biomass C:N:P ratios were highly constrained. Soil accessible inorganic nitrogen played an important role in driving plant and microbial nutrient and stoichiometry. Our results demonstrated that the different responses of C, N, and P contents in plant-soil-microbe lead to shifts in C:N:P stoichiometric ratio. Nevertheless, plants and soil microbes exhibited strong stoichiometric homeostasis. Collectively, our study provides new insight into biogeochemical responses to the successional recovery of degraded alpine grassland on the Qinghai-Tibetan Plateau from a stoichiometric perspective.

Animal body size distribution influences the ratios of nutrients supplied to plants.

Nutrients released through herbivore feces have the potential to influence plant-available nutrients and affect primary productivity. However, herbivore species use nutrients in set stoichiometric ratios that vary with body size. Such differences in the ratios at which nutrients are used leads to differences in the ratios at which nutrients are deposited through feces. Thus, local environmental factors that affect the average body size of an herbivore community (such as predation risk and food availability) influence the ratios at which fecal nutrients are supplied to plants. Here, we assess the relationship between herbivore body size and the nitrogen-to-phosphorus ratios of herbivore feces. We examine how shifts in the average body size of an herbivore community alter the ratios at which nitrogen and phosphorus are supplied to plants and test whether such differences in the stoichiometry of nutrient supply propagate through plants. We show that dung from larger-bodied herbivores contain lower quantities of phosphorus per unit mass and were higher in N:P ratio. We demonstrate that spatial heterogeneity in visibility (a proxy for predation risk and/or food availability) and rainfall (a proxy for food availability), did not affect the overall amount of feces deposited but led to changes in the average body size of the defecating community. Feces deposited in areas of higher rainfall and reduced visibility originated from larger herbivores and were higher in N:P ratios. This indicates that processes that change the size distribution of herbivore communities, such as predation or size-biased extinction, have the potential to alter the nutrient landscape for plants.

Marine heatwaves of differing intensities lead to distinct patterns in seafloor functioning.

Marine heatwaves (MHWs) are increasing in frequency and intensity due to climate change. Several well-documented effects of heatwaves on community structure exist, but examples of their effect on functioning of species, communities or ecosystems remain scarce. We tested the effects of short-term, moderate and strong MHWs on macrofauna bioturbation and associated solute fluxes as examples of ecosystem functioning. We also measured macrofaunal excretion rates to assess effects of temperature on macrofauna metabolism. For this experiment, we used unmanipulated sediment cores with natural animal communities collected from a muddy location at 32 m depth in the northern Baltic Sea. Despite the mechanistic effect of bioturbation remaining unchanged between the treatments, there were significant differences in oxygen consumption, solute fluxes and excretion. Biogeochemical and biological processes were boosted by the moderate heatwave, whereas biogeochemical cycling seemed to decrease under a strong heatwave. A prolonged, moderate heatwave could possibly lead to resource depletion if primary production cannot meet the demands of benthic consumption. By contrast, decreased degradation activities under strong heatwaves could lead to a build-up of organic material and potentially hypoxia. The strong variability and the complexity of the response highlight the context dependency of these processes complicating future predictions.

Detrital Carbonate Minerals in Earth's Element Cycles.

We investigate if the commonly neglected riverine detrital carbonate fluxes might reconciliate several chemical mass balances of the global ocean. Particulate inorganic carbon (PIC) concentrations in riverine suspended sediments, that is, carbon contained by these detrital carbonate minerals, were quantified at the basin and global scale. Our approach is based on globally representative data sets of riverine suspended sediment composition, catchment properties, and a two-step regression procedure. The present-day global riverine PIC flux is estimated at 3.1 ± 0.3 Tmol C/y (13% of total inorganic carbon export and 4% of total carbon export) with a flux-weighted mean concentration of 0.26 ± 0.03 wt%. The flux prior to damming was 4.1 ± 0.5 Tmol C/y. PIC fluxes are concentrated in limestone-rich, rather dry and mountainous catchments of large rivers near Arabia, South East Asia, and Europe with 2.2 Tmol C/y (67.6%) discharged between 15°N and 45°N. Greenlandic and Antarctic meltwater discharge and ice-rafting additionally contribute 0.8 ± 0.3 Tmol C/y. This amount of detrital carbonate minerals annually discharged into the ocean implies a significant contribution of calcium (∼4.75 Tmol Ca/y) and alkalinity fluxes (∼10 Tmol (eq)/y) to marine mass balances and moderate inputs of strontium (∼5 Gmol Sr/y) based on undisturbed riverine and cryospheric inputs and a dolomite/calcite ratio of 0.1. Magnesium fluxes (∼0.25 Tmol Mg/y), mostly hosted by less-soluble dolomite, are rather negligible. These unaccounted fluxes help in elucidating respective marine mass balances and potentially alter conclusions based on these budgets.

Single Strain-Triggered Biogeochemical Cycle of Arsenic.

The microbial metabolism of arsenic plays a prominent role in governing the biogeochemical cycle of arsenic. Although diverse microbes are known to be involved in the redox transformation of inorganic arsenic, the underlying mechanisms about the arsenic redox cycle mediated by a single microbial strain remain unclear yet. Herein, we discover that Shewanella putrefaciens CN32, a well-known arsenate-respiring and dissimilatory metal-reducing bacterium, could mediate the reversible arsenic redox transformation under aerobic conditions. Genetic analysis shows that S. putrefaciens CN32 contains both ars and arr operon but lacks an As(III) oxidase encoding gene. Arsenic(V) reduction tests demonstrate that the ars operon is advantageous but not essential for As(V) respiration in S. putrefaciens CN32. The Arr complex encoded by the arr operon not only plays a crucial role in arsenate respiration under anaerobic conditions but also participates in the sequential process of As(V) reduction and As(III) oxidation under aerobic conditions. The Arr enzyme also contributes to the microbial As(III) resistance. The expression and catalysis directionality of Arr in S. putrefaciens CN32 are regulated by the carbon source types. Our results highlight the complexity of arsenic redox biotransformation in environments and provide new insights into the important contribution of Arr to the As biogeochemical cycle in nature.

Metagenome-Assembled Genomes of Novel Taxa from an Acid Mine Drainage Environment.

Acid mine drainage (AMD) is a global problem in which iron sulfide minerals oxidize and generate acidic, metal-rich water. Bioremediation relies on understanding how microbial communities inhabiting an AMD site contribute to biogeochemical cycling. A number of studies have reported community composition in AMD sites from 16S rRNA gene amplicons, but it remains difficult to link taxa to function, especially in the absence of closely related cultured species or those with published genomes. Unfortunately, there is a paucity of genomes and cultured taxa from AMD environments. Here, we report 29 novel metagenome-assembled genomes from Cabin Branch, an AMD site in the Daniel Boone National Forest, Kentucky, USA. The genomes span 11 bacterial phyla and one archaeal phylum and include taxa that contribute to carbon, nitrogen, sulfur, and iron cycling. These data reveal overlooked taxa that contribute to carbon fixation in AMD sites as well as uncharacterized Fe(II)-oxidizing bacteria. These data provide additional context for 16S rRNA gene studies, add to our understanding of the taxa involved in biogeochemical cycling in AMD environments, and can inform bioremediation strategies. IMPORTANCE Bioremediating acid mine drainage requires understanding how microbial communities influence geochemical cycling of iron and sulfur and biologically important elements such as carbon and nitrogen. Research in this area has provided an abundance of 16S rRNA gene amplicon data. However, linking these data to metabolisms is difficult because many AMD taxa are uncultured or lack published genomes. Here, we present metagenome-assembled genomes from 29 novel AMD taxa and detail their metabolic potential. These data provide information on AMD taxa that could be important for bioremediation strategies, including taxa that are involved in cycling iron, sulfur, carbon, and nitrogen.

Bacteria and Metabolic Potential in Karst Caves Revealed by Intensive Bacterial Cultivation and Genome Assembly.

Karst caves are widely distributed subsurface systems, and the microbiomes therein are proposed to be the driving force for cave evolution and biogeochemical cycling. In past years, culture-independent studies on the microbiomes of cave systems have been conducted, yet intensive microbial cultivation is still needed to validate the sequence-derived hypothesis and to disclose the microbial functions in cave ecosystems. In this study, the microbiomes of two karst caves in Guizhou Province in southwest China were examined. A total of 3,562 bacterial strains were cultivated from rock, water, and sediment samples, and 329 species (including 14 newly described species) of 102 genera were found. We created a cave bacterial genome collection of 218 bacterial genomes from a karst cave microbiome through the extraction of 204 database-derived genomes and de novo sequencing of 14 new bacterial genomes. The cultivated genome collection obtained in this study and the metagenome data from previous studies were used to investigate the bacterial metabolism and potential involvement in the carbon, nitrogen, and sulfur biogeochemical cycles in the cave ecosystem. New N2-fixing Azospirillum and alkane-oxidizing Oleomonas species were documented in the karst cave microbiome. Two pcaIJ clusters of the ß-ketoadipate pathway that were abundant in both the cultivated microbiomes and the metagenomic data were identified, and their representatives from the cultivated bacterial genomes were functionally demonstrated. This large-scale cultivation of a cave microbiome represents the most intensive collection of cave bacterial resources to date and provides valuable information and diverse microbial resources for future cave biogeochemical research.IMPORTANCE Karst caves are oligotrophic environments that are dark and humid and have a relatively stable annual temperature. The diversity of bacteria and their metabolisms are crucial for understanding the biogeochemical cycling in cave ecosystems. We integrated large-scale bacterial cultivation with metagenomic data mining to explore the compositions and metabolisms of the microbiomes in two karst cave systems. Our results reveal the presence of a highly diversified cave bacterial community, and 14 new bacterial species were described and their genomes sequenced. In this study, we obtained the most intensive collection of cultivated microbial resources from karst caves to date and predicted the various important routes for the biogeochemical cycling of elements in cave ecosystems.

Heat stress decreases the diversity, abundance and functional potential of coral gas emissions.

Terrestrial ecosystems emit large quantities of biogenic volatile organic compounds (BVOCs), many of which play important roles in abiotic stress responses, pathogen and grazing defences, inter- and intra-species communications, and climate regulation. Conversely, comparatively little is known about the diversity and functional potential of BVOCs produced in the marine environment, especially in highly productive coral reefs. Here we describe the first 'volatilomes' of two common reef-building corals, Acropora intermedia and Pocillopora damicornis, and how the functional potential of their gaseous emissions is altered by heat stress events that are driving rapid deterioration of coral reef ecosystems worldwide. A total of 87 BVOCs were detected from the two species and the chemical richness of both coral volatilomes-particularly the chemical classes of alkanes and carboxylic acids-decreased during heat stress by 41% and 62% in A. intermedia and P. damicornis, respectively. Across both coral species, the abundance of individual compounds changed significantly during heat stress, with the majority (>86%) significantly decreasing compared to control conditions. Additionally, almost 60% of the coral volatilome (or 52 BVOCs) could be assigned to four key functional groups based on their activities in other species or systems, including stress response, chemical signalling, climate regulation and antimicrobial activity. The total number of compounds assigned to these functions decreased significantly under heat stress for both A. intermedia (by 35%) and P. damicornis (by 64%), with most dramatic losses found for climatically active BVOCs in P. damicornis and antimicrobial BVOCs in A. intermedia. Together, our observations suggest that future heat stress events predicted for coral reefs will reduce the diversity, quantity and functional potential of BVOCs emitted by reef-building corals, potentially further compromising the healthy functioning of these ecosystems.

Microbial Diversity of Deep-Sea Ferromanganese Crust Field in the Rio Grande Rise, Southwestern Atlantic Ocean.

Seamounts are often covered with Fe and Mn oxides, known as ferromanganese (Fe-Mn) crusts. Future mining of these crusts is predicted to have significant effects on biodiversity in mined areas. Although microorganisms have been reported on Fe-Mn crusts, little is known about the role of crusts in shaping microbial communities. Here, we investigated microbial communities based on 16S rRNA gene sequences retrieved from Fe-Mn crusts, coral skeleton, calcarenite, and biofilm at crusts of the Rio Grande Rise (RGR). RGR is a prominent topographic feature in the deep southwestern Atlantic Ocean with Fe-Mn crusts. Our results revealed that crust field of the RGR harbors a usual deep-sea microbiome. No differences were observed on microbial community diversity among Fe-Mn substrates. Bacterial and archaeal groups related to oxidation of nitrogen compounds, such as Nitrospirae, Nitrospinae phyla, Candidatus Nitrosopumilus within Thaumarchaeota group, were present on those substrates. Additionally, we detected abundant assemblages belonging to methane oxidation, i.e., Methylomirabilales (NC10) and SAR324 (Deltaproteobacteria). The chemolithoautotrophs associated with ammonia-oxidizing archaea and nitrite-oxidizing bacteria potentially play an important role as primary producers in the Fe-Mn substrates from RGR. These results provide the first insights into the microbial diversity and potential ecological processes in Fe-Mn substrates from the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region.

The Pedosphere as a Sink, Source, and Record of Anthropogenic and Natural Arsenic Atmospheric Deposition.

The Anthropocene has led to global-scale contamination of the biosphere through diffuse atmospheric dispersal of arsenic. This review considers the sources arsenic to soils and its subsequent fate, identifying key knowledge gaps. There is a particular focus on soil classification and stratigraphy, as this is central to the topic under consideration. For Europe and North America, peat core chrono-sequences record massive enhancement of arsenic depositional flux from the onset of the Industrial Revolution to the late 20th century, while modern mitigation efforts have led to a sharp decline in emissions. Recent arsenic wet and dry depositional flux measurements and modern ice core records suggest that it is South America and East Asia that are now primary global-scale polluters. Natural sources of arsenic to the atmosphere are primarily from volcanic emissions, aeolian soil dust entrainment, and microbial biomethylation. However, quantifying these natural inputs to the atmosphere, and subsequent redeposition to soils, is only starting to become better defined. The pedosphere acts as both a sink and source of deposited arsenic. Soil is highly heterogeneous in the natural arsenic already present, in the chemical and biological regulation of its mobility within soil horizons, and in interaction with climatic and geomorphological settings. Mineral soils tend to be an arsenic sink, while organic soils act as both a sink and a source. It is identified here that peatlands hold a considerable amount of Anthropocene released arsenic, and that this store can be potentially remobilized under climate change scenarios. Also, increased ambient temperature seems to cause enhanced arsine release from soils, and potentially also from the oceans, leading to enhanced rates of arsenic biogeochemical cycling through the atmosphere. With respect to agriculture, rice cultivation was identified as a particular concern in Southeast Asia due to the current high arsenic deposition rates to soil, the efficiency of arsenic assimilation by rice grain, and grain yield reduction through toxicity.

Influence of pH and Dissolved Organic Matter on Iron Speciation and Apparent Iron Solubility in the Peruvian Shelf and Slope Region.

The chemical speciation of iron (Fe) in oceans is influenced by ambient pH, dissolved oxygen, and the concentrations and strengths of the binding sites of dissolved organic matter (DOM). Here, we derived new nonideal competitive adsorption (NICA) constants for Fe(III) binding to marine DOM via pH-Fe titrations. We used the constants to calculate Fe(III) speciation and derive the apparent Fe(III) solubility (SFe(III)app) in the ambient water column across the Peruvian shelf and slope region. We define SFe(III)app as the sum of aqueous inorganic Fe(III) species and Fe(III) bound to DOM at a free Fe (Fe3+) concentration equal to the limiting solubility of Fe hydroxide (Fe(OH)3(s)). A ca. twofold increase in SFe(III)app in the oxygen minimum zone (OMZ) compared to surface waters is predicted. The increase results from a one order of magnitude decrease in H+ concentration which impacts both Fe(III) hydroxide solubility and organic complexation. A correlation matrix suggests that changes in pH have a larger impact on SFe(III)app and Fe(III) speciation than DOM in this region. Using Fe(II) measurements, we calculated ambient DFe(III) and compared the value with the predicted SFe(III)app. The underlying distribution of ambient DFe(III) largely reflected the predicted SFe(III)app, indicating that decreased pH as a result of OMZ intensification and ocean acidification may increase SFe(III)app with potential impacts on surface DFe inventories.