Effect of conventional and biodegradable microplastics on the soil-soybean system: A perspective on rhizosphere microbial community and soil element cycling.

As an exogenous carbon input, microplastics (MPs), especially biodegradable MPs, may significantly disrupt soil microbial communities and soil element cycling (CNPS cycling), but few studies have focused on this. Here, we focused on assessing the effects of conventional low-density polyethylene (LDPE), biodegradable polybutylene adipate terephthalate (PBAT), and polylactic acid (PLA) MPs on rhizosphere microbial communities and CNPS cycling in a soil-soybean system. The results showed that PBAT-MPs and PLA-MPs were more detrimental to soybean growth than LDPE-MPs, resulting in a reduction in shoot nitrogen (14.05% and 11.84%) and shoot biomass (33.80% and 28.09%) at the podding stage. In addition, dissolved organic carbon (DOC) increased by 20.91% and 66.59%, while nitrate nitrogen (NO3--N) significantly decreased by 56.91% and 69.65% in soils treated with PBAT-MPs and PLA-MPs, respectively. PBAT-MPs and PLA-MPs mainly enhanced copiotrophic bacteria (Proteobacteria) and suppressed oligotrophic bacteria (Verrucomicrobiota, Gemmatimonadota, etc.), increasing the abundance of CNPS cycling-related functional genes. LDPE-MPs tended to enrich oligotrophic bacteria (Verrucomicrobiota, etc.) and decrease the abundance of CNPS cycling-related functional genes. Correlation analysis revealed that MPs with different degradation properties selectively affected the composition and function of the bacterial community, resulting in changes in the availability of soil nutrients (especially NO3--N). Redundancy analysis further indicated that NO3--N was the primary constraining factor for soybean growth. This study provides a new perspective for revealing the underlying ecological effects of MPs on soil-plant systems.

A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants.

The concentration of viruses in sewage sludge is significantly higher (10-1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well as their role in the carbon, nitrogen, and phosphorus cycles remain poorly understood. In this study, we employed a shotgun metagenomic approach to investigate the pathogenic bacteria and viral composition and function in two wastewater treatment plants located on a campus. Our analysis revealed the presence of 1334 amplicon sequence variants (ASVs) across six sludge samples, with 242 ASVs (41.22% of total reads) identified as pathogenic bacteria. Arcobacter was found to be the most dominant pathogen accounting for 6.79% of total reads. The virome analysis identified 613 viral genera with Aorunvirus being the most abundant genus at 41.85%. Approximately 0.66% of these viruses were associated with human and animal diseases. More than 60% of the virome consisted of lytic phages. Host prediction analysis revealed that the phages primarily infected Lactobacillus (37.11%), Streptococcus (21.11%), and Staphylococcus (7.11%). Furthermore, our investigation revealed an abundance of auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and phosphorus cycling within the virome. We also detected a total of 113 antibiotic resistance genes (ARGs), covering major classes of antibiotics across all samples analyzed. Additionally, our findings indicated the presence of virulence factors including the clpP gene accounting for approximately 4.78%, along with toxin genes such as the RecT gene representing approximately 73.48% of all detected virulence factors and toxin genes among all samples analyzed. This study expands our understanding regarding both pathogenic bacteria and viruses present within sewage sludge while providing valuable insights into their ecological functions.

Green manuring relocates microbiomes in driving the soil functionality of nitrogen cycling to obtain preferable grain yields in thirty years.

Fertilizers are widely used to produce more food, inevitably altering the diversity and composition of soil organisms. The role of soil biodiversity in controlling multiple ecosystem services remains unclear, especially after decades of fertilization. Here, we assess the contribution of the soil functionalities of carbon (C), nitrogen (N), and phosphorus (P) cycling to crop production and explore how soil organisms control these functionalities in a 33-year field fertilization experiment. The long-term application of green manure or cow manure produced wheat yields equivalent to those obtained with chemical N, with the former providing higher soil functions and allowing the functionality of N cycling (especially soil N mineralization and biological N fixation) to control wheat production. The keystone phylotypes within the global network rather than the overall microbial community dominated the soil multifunctionality and functionality of C, N, and P cycling across the soil profile (0-100 cm). We further confirmed that these keystone phylotypes consisted of many metabolic pathways of nutrient cycling and essential microbes involved in organic C mineralization, N2O release, and biological N fixation. The chemical N, green manure, and cow manure resulted in the highest abundances of amoB, nifH, and GH48 genes and Nitrosomonadaceae, Azospirillaceae, and Sphingomonadaceae within the keystone phylotypes, and these microbes were significantly and positively correlated with N2O release, N fixation, and organic C mineralization, respectively. Moreover, our results demonstrated that organic fertilization increased the effects of the network size and keystone phylotypes on the subsoil functions by facilitating the migration of soil microorganisms across the soil profiles and green manure with the highest migration rates. This study highlights the importance of the functionality of N cycling in controlling crop production and keystone phylotypes in regulating soil functions, and provides selectable fertilization strategies for maintaining crop production and soil functions across soil profiles in agricultural ecosystems.

Seasonal variations of biofilm C, N and S cycling genes in a pilot-scale chlorinated drinking water distribution system.

Biofilms in drinking water distribution systems (DWDS) host diverse microorganisms. However, the functional attributes of DWDS biofilms and their associations with seasonality remain unclear. This study aims to characterize variations in the microbial metabolic traits of DWDS biofilms collected during different seasons, using a pilot-scale DWDS in dark under plug-flow conditions during one-year operation period. Network analysis was used to predict the functional gene hosts. The overall functional attributes determined by shotgun metagenomics exhibited significant differences among seasons. Genes associated with aromatic metabolism, fatty acid biosynthesis and degradation, and capsular extracellular polymeric substance (EPS) were significantly upregulated in summer owing to the higher temperatures and chlorine in the influent of the DWDS. Moreover, the pathways associated with nitrogen, sulfur, glycolysis, and tricarboxylic acid (TCA) cycling, as well as carbon fixation were reconstructed and displayed according to the sampling season. Nitrogen reduction pathways [dissimilatory nitrate reduction to ammonium (DNRA) 73 %, assimilatory nitrate reduction to ammonium (ANRA) 21 %] were identified in DWDS biofilms, but nitrogen oxidation pathways were not. Sulfur cycling were involved in diverse pathways and genes. Glycolysis and TCA cycling offered electron donors and energy sources for nitrogen and sulfur reduction in biofilms. Carbon fixation was observed in DWDS biofilms, with the predominant pathway for fixing carbon dioxide being the reductive citrate cycle (38 %). Constructed functional gene networks composed of carbon, nitrogen, and sulfur cycling-related genes demonstrated synergistic effects (Positive proportion: 63.52-71.09 %). In addition, from spring to autumn, the network complexity decreased and network modularity increased. The assembly mechanism of carbon, nitrogen and sulfur cycling-related genes was driven by stochastic processes for all samples. These results highlight the diverse functional genes in DWDS biofilms, their synergetic interrelationships, and the seasonality effect on functional attributes.

Metagenome-assembled genomes reveal carbohydrate degradation and element metabolism of microorganisms inhabiting Tengchong hot springs, China.

A hot spring is a distinctive aquatic environment that provides an excellent system to investigate microorganisms and their function in elemental cycling processes. Previous studies of terrestrial hot springs have been mostly focused on the microbial community, one special phylum or category, or genes involved in a particular metabolic step, while little is known about the overall functional metabolic profiles of microorganisms inhabiting the terrestrial hot springs. Here, we analyzed the microbial community structure and their functional genes based on metagenomic sequencing of six selected hot springs with different temperature and pH conditions. We sequenced a total of 11 samples from six hot springs and constructed 162 metagenome-assembled genomes (MAGs) with completeness above 70% and contamination lower than 10%. Crenarchaeota, Euryarchaeota and Aquificae were found to be the dominant phyla. Functional annotation revealed that bacteria encode versatile carbohydrate-active enzymes (CAZYmes) for the degradation of complex polysaccharides, while archaea tend to assimilate C1 compounds through carbon fixation. Under nitrogen-deficient conditions, there were correspondingly fewer genes involved in nitrogen metabolism, while abundant and diverse set of genes participating in sulfur metabolism, particularly those associated with sulfide oxidation and thiosulfate disproportionation. In summary, archaea and bacteria residing in the hot springs display distinct carbon metabolism fate, while sharing the common energy preference through sulfur metabolism. Overall, this research contributes to a better comprehension of biogeochemistry of terrestrial hot springs.

Effects of long-term no-tillage on the functional potential of microorganisms involved in the nitrogen, phosphorus and sulfur cycles of black soil.

Understanding the effects of different tillage practices on functional microbial abundance and composition in nitrogen (N), phosphorus (P) and sulfur (S) cycles are essential for the sustainable utilization of black soils. Based on an 8-year field experiment located in Changchun, Jilin Province, we analyzed the abundance and composition of N, P and S cycling microorganisms and their driving factors in different depths of black soil under no til-lage (NT) and conventional tillage (CT). Results showed that compared with CT, NT significantly increased soil water content (WC) and microbial biomass carbon (MBC) at soil depth of 0-20 cm. Compared with CT, NT significantly increased the abundances of functional and encoding genes related to N, P and S cycling, including the nosZ gene encoding N2O reductase, the ureC gene performing organic nitrogen ammoniation, the nifH gene encoding nitrogenase ferritin, the functional genes phnK and phoD driving organic phosphorus mineralization, the encoding pyrroloquinoline quinone synthase ppqC gene and the encoding exopolyphosphate esterase ppX gene, and the soxY and yedZ genes driving sulfur oxidation. The results of variation partitioning analysis and redundancy analysis showed that soil basic properties were the main factors affecting the microbial composition of N, P and S cycle functions (the total interpretation rate was 28.1%), and that MBC and WC were the most important drivers of the functional potential of soil microorganisms in N, P and S cycling. Overall, long-term no tillage could increase the abundance of functional genes of soil microorganisms by affecting soil environment. From the perspective of molecular biology, our results elucidated that no tillage could be used as an effective soil management measure to improve soil health and maintain green agricultural development.

[QMEC-based Analysis of the Soil Microbial Functional Potentials across Different Tibetan Plateau Glacier Forelands].

Soil microorganisms dominate the biogeochemical cycles of elements in glacier forelands, which continue to expand due to the climate warming. We analyzed the soil microbial functional characteristics among three types of glacier forelands on the Tibetan Plateau: Yulong Glacier (Y), a temperate glacier; Tianshan Urumqi Glacier No.1 (T), a sub-continental glacier; and Laohugou Glacier No.12 (L), a continental glacier. Here, soil microbial functional genes were quantified using quantitative microbial element cycling technology (QMEC). We found that, in the three glacier forelands, the abundances of soil microbial functional genes related to hemicellulose degradation and reductive acetyl-CoA pathway were highest compared with other carbon-related functional genes. The main nitrogen cycling genes were involved in ammonification. The functional genes of the phosphorus cycle and sulfur cycle were related to organic phosphate mineralization and sulfur oxidation. Furthermore, the soils of the temperate glacier foreland with better hydrothermal conditions had the most complex microbial functional gene structure and the highest functional potentials, followed by those of the soils of continental glacier foreland with the driest environment. These significant differences in soil microbial functional genes among the three types of glacier forelands verified the impacts of geographic difference on microbial functional characteristics, as well as providing a basis for the study of soil microbial functions and biogeochemical cycles in glacier forelands.

Fire-induced geochemical changes in soil: Implication for the element cycling.

Soils play an essential role in supporting and sustaining life on this planet. In fire-impacted environments, fire causes considerable changes to the soil, especially in the various elements. The present work provides a comprehensive and up-to-date review of the effect of fire on soil geochemistry, and its impact on the cycling of different biogenic, major, minor, and trace elements in the soil. Results from both natural and experimental fires (field-scale and lab-scale) are considered in this review. The temperature at which mineral transformation occurs in the soil during fires is summarised. The review suggests that fires can significantly alter mobility and hence, the cycling of many elements in fire-affected regions. Change in speciation of elements following fires risks formation and/or increased availability of the toxic forms of elements in the soil. The unique physical, chemical, and biological conditions observed during fires make many unlikely reactions more likely. However, the information available in the literature is often fire, vegetation, and element specific. More studies on this topic by changing these three variables will improve our understanding of changes in the soil caused by fire. Hence, with fires being touted to increase global presence in the coming years, more studies on understanding their effects on soils are recommended.

Nitrate Controls on the Extent and Type of Metal Retention in Fine-Grained Sediments of a Simulated Aquifer.

Aquifer groundwater quality is largely controlled by sediment composition and physical heterogeneity, which commonly sustains a unique redox gradient pattern. Attenuation of heavy metals within these heterogeneous aquifers is reliant on multiple factors, including redox conditions and redox-active species that can further influence biogeochemical cycling. Here, we simulated an alluvial aquifer system using columns filled with natural coarse-grained sediments and two domains of fine-grained sediment lenses. Our goal was to examine heavy metal (Ni and Zn) attenuation within a complex aquifer network and further explore nitrate-rich groundwater conditions. The fine-grained sediment lenses sustained reducing conditions and served as a sink for Ni sequestration─in the form of Ni-silicates, Ni-organic matter, and a dominant Ni-sulfide phase. The silicate clay and sulfide pools were also important retention mechanisms for Zn; however, Ni was associated more extensively with organic matter compared to Zn, which formed layered double hydroxides. Nitrate-rich conditions promoted denitrification within the lenses that was coupled to the oxidation of Fe(II) and the concomitant precipitation of an Fe(III) phase with higher structural distortion. A decreased metal sulfide pool also resulted, where nitrate-rich conditions generated an average 20% decrease in solid-phase Ni, Zn, and Fe. Ultimately, nitrate plays a significant role in the aquifer's biogeochemical cycling and the capacity to retain heavy metals.

Trace elements apportionment in forage, soil, and livestock in rangeland ecosystems along climatic gradients.

BACKGROUND: Alpine meadows, typical steppes, and deserts are among the globally important rangeland types that are generally distributed along temperature and precipitation gradients. Mineral losses caused by grazing are one of the key factors that can lead to instability or even degradation of these rangeland ecosystems. METHODS: We examined the concentrations of Cu, Fe, Mn, and Zn in soil, forage, and livestock dungs from diverse rangeland types in northwest China, to determine the relationships between these trace elements (TEs) concentrations and climatic factors (i.e., temperature, precipitation, and humidity), and to evaluate the potential risks of TEs deficiencies or excesses in these rangeland ecosystems. RESULTS: Forage Zn concentrations in forage of all three types of rangeland, and Cu concentrations in forage of the alpine meadow did not meet the growth requirements of grazing livestock. Concentrations of Cu, Fe, and Mn in forage and Fe, Mn, and Zn in livestock dungs had quadratic parabola relationships with temperature, precipitation, and humidity, but the relationships between climate factors and Cu, Fe, and Mn concentrations in soil were not significant. In addition, the abilities of the plant to absorb Cu, Fe, and Zn from soil were stronger in the typical steppe than that in the alpine meadows and desert. Also, the abilities of livestock to return TEs to soil were stronger in the alpine meadow than that in the typical steppe and desert. CONCLUSION: We derived a conceptual mode that the ratio of TE concentrations of the plant to soil and of livestock dung to forage represents the abilities of plants to absorb TEs from the soil matrix and livestock to return TEs to soil or to absorb TEs from forage, respectively. Results indicate potentially more serious risks of TEs deficiencies, especially that of Zn than previously considered in typical steppes and desert rangelands.

Herbivores in Arctic ecosystems: Effects of climate change and implications for carbon and nutrient cycling.

Arctic terrestrial herbivores influence tundra carbon and nutrient dynamics through their consumption of resources, waste production, and habitat-modifying behaviors. The strength of these effects is likely to change spatially and temporally as climate change drives shifts in herbivore abundance, distribution, and activity timing. Here, we review how herbivores influence tundra carbon and nutrient dynamics through their consumptive and nonconsumptive effects. We also present evidence for herbivore responses to climate change and discuss how these responses may alter the spatial and temporal distribution of herbivore impacts. Several current knowledge gaps limit our understanding of the changing functional roles of herbivores; these include limited characterization of the spatial and temporal variability in herbivore impacts and of how herbivore activities influence the cycling of elements beyond carbon. We conclude by highlighting approaches that will promote better understanding of herbivore effects on tundra ecosystems, including their integration into existing biogeochemical models, new applications of remote sensing techniques, and the continued use of distributed experiments.

Zn isotope fractionation in laterites from Yunnan province, southwest China: Implications for the Zn cycles and its environmental impacts in (sub-) tropics.

The weathering and development of laterites can influence trace element cycling in (sub-) tropics. Zinc (Zn) is a ubiquitous trace metal that involves both abiotic and biotic processes in soils. To explore Zn behavior in laterites, Zn cycling in (sub-) tropics, and the environmental impacts, Zn isotope systematics were presented for two laterite profiles from Yunnan province, southwest China. The laterite samples exhibit the δ66Zn of 0.02 ‰-0.56 ‰, indicating a light shift of Zn isotope ratios (Δ66Znlaterite-parent rock = -0.47 ‰-0.07 ‰) relative to bulk parent granite. This observation is attributed to the preferential preservation of light Zn isotopes on the surface of secondary Fe oxides. As a result, laterites are likely to control the instantaneous riverine δ66Zn in (sub-) tropical regions heavier than unweathered rocks. The isotopic signature of different vegetation covered soils show that shrub-covered soils are stronger leached (average τZn = -0.61) and have a smaller Δ66Znlaterite-parent rock (=-0.15 ‰), relative to forest-covered soils (=-0.20 ‰). Due to the strong loss of Zn (average τZn = -0.61 to -0.12) and large amounts of low-bioavailable Zn preserved in oxides, the micronutrient supplies for plant growth are difficult to maintain and need more fertilization. This study is helpful for a better understanding of global Zn cycling and the management of micronutrients in (sub-) tropical soil-plant systems.

Cryptic Sulfur and Oxygen Cycling Potentially Reduces N2O-Driven Greenhouse Warming: Underlying Revision Need of the Nitrogen Cycle.

Increasing global deoxygenation has widely formed oxygen-limited biotopes, altering the metabolic pathways of numerous microbes and causing a large greenhouse effect of nitrous oxide (N2O). Although there are many sources of N2O, denitrification is the sole sink that removes N2O from the biosphere, and the low-level oxygen in waters has been classically thought to be the key factor regulating N2O emissions from incomplete denitrification. However, through microcosm incubations with sandy sediment, we demonstrate here for the first time that the stress from oxygenated environments does not suppress, but rather boosts the complete denitrification process when the sulfur cycle is actively ongoing. This study highlights the potential of reducing N2O-driven greenhouse warming and fills a gap in pre-cognitions on the nitrogen cycle, which may impact our current understanding of greenhouse gas sinks. Combining molecular techniques and kinetic verification, we reveal that dominant inhibitions in oxygen-limited environments can interestingly undergo triple detoxification by cryptic sulfur and oxygen cycling, which may extensively occur in nature but have been long neglected by researchers. Furthermore, reviewing the present data and observations from natural and artificial ecosystems leads to the necessary revision needs of the global nitrogen cycle.

Genome- and community-level interaction insights into the ecological role of archaea in rare earth element mine drainage in South China.

Microbial communities play crucial roles in mine drainage generation and remediation. Despite the wide distribution of archaea in the mine ecosystem, their diversity and ecological roles remain less understood than bacteria. Here, we retrieved 56 archaeal metagenome-assembled genomes from a river impacted by rare earth element (REE) mining activities in South China. Genomic analysis showed that archaea represented four distinct lineages, including phyla of Thaumarchaeota, Micrarchaeota, Nanoarchaeota and Thermoplasmata. These archaea represented a considerable fraction (up to 40%) of the total prokaryote community, which might contribute to nitrogen and sulfur cycling in the REE mine drainage. Reconstructed metabolic potential among diverse archaea taxa revealed that archaea were involved in the network of ammonia oxidation, denitrification, sulfate redox reaction, and required substrates supplied by other community members. As the dominant driver of ammonia oxidation, Thaumarchaeota might provide substrates to support the survival of two nano-sized archaea belonging to Micrarchaeota and Nanoarchaeota. Despite the absence of biosynthesis pathways for amino acids and nucleotides, the potential capacity for nitrite reduction (nirD) was observed in Micrarchaeota, indicating that these nano-sized archaea encompassed diverse metabolisms. Moreover, Thermoplasmata, as keystone taxa in community, might be the main genetic donor for the other three archaeal phyla, transferring many environmental resistance related genes (e.g., V/A-type ATPase and Vitamin B12-transporting ATPase). The genetic interactions within archaeal community through horizontal gene transfer might be the key to the formation of archaeal resistance and functional partitioning. This study provides putative metabolic and genetic insights into the diverse archaea taxa from community-level perspectives, and highlights the ecological roles of archaea in REE contaminated aquatic environment.

Uptake of Cd, Pb, U, and Zn by plants in floodplain pollution hotspots contributes to secondary contamination.

Willows, woody plants of genus Salix common in floodplains of temperate regions, act as plant pumps and translocate the Cd and Zn in the soil profiles of uncontaminated and weakly contaminated floodplains from the sediment bulk to the top strata. We suggest this process occurs because the Cd and Zn concentrations in willow leaves exceed those in the sediments. Senescing foliage of plant species common in floodplains can increase the Cd and Zn ratios as compared to other elements (Pb and common 'lithogenic elements' such as Al) in the top strata of all floodplains, including those that have been severely contaminated. The top enrichment is caused by the root uptake of specific elements by growing plants, which is followed by foliage deposition. Neither the shallow groundwater nor the plant foliage shows that Cd, Zn, and Pb concentrations are related to those in the sediments, but they clearly reflect the shallow groundwater pH, with the risk element mobilised by the acidity that is typical for the subsurface sediments in floodplains. The effect that plants have on the Pb in floodplains is significantly lower than that observed for Cd and Zn, while U can be considered even less mobile than Pb. Groundwater and plant leaves can contribute to secondary contamination with Cd and Zn from floodplain pollution hotspots, meaning that plants can accumulate these elements on the floodplain surface or even return them back to the fluvial transport, even if bank erosion would not occur. For Pb and U at the sites studied, these risks were negligible.

Persistent contamination of polycyclic aromatic hydrocarbons (PAHs) and phthalates linked to the shift of microbial function in urban river sediments.

Urban rivers were heavily polluted, which resulted in blackening and odorization (i.e., black-odor rivers). Nevertheless, very limited information is available on sediment contamination levels of black-odor rivers and their linkage to the patterns of microbial functional genes. This study investigated distribution of polycyclic aromatic hydrocarbons (PAHs) and phthalates (PAEs) and their linkages to bacterial community and related functional genes in river sediments. The results demonstrate that higher average levels of ∑16PAHs (1405 µg/kg, dry weight) and ∑6PAEs (7120 µg/kg) were observed in sediments from heavy black-odor rivers than the moderate ones (∑16PAHs: 462 µg/kg; ∑6PAEs: 2470 µg/kg). The taxon composition and diversities of bacterial community in sediments varied with significantly lower diversity indices in heavy black-odor rivers than moderate ones. Sediments from heavy black-odor rivers enriched certain PAH and PAE degrading bacteria and genes. Unfortunately, PAH and PAE contamination demonstrated negative influences on nitrogen and phosphorus metabolism related bacteria and function genes but significant positive influences on certain sulfur metabolism related bacterial taxa and sulfur reduction gene, which might cause nitrogen and phosphorus accumulation and black-odor phenomenon in heavy black-odor rivers. This study highlights PAH and PAE contamination in urban rivers may shift bacterial community and detrimentally affect their ecological functions.

Interactions between Escherichia coli survival and manganese and iron oxides in water under freeze-thaw.

Pathogenic survivals were dramatically affected by Fe3+ and Mn2+ under freeze-thaw (FT), and the dissolutions of manganese and iron oxides (MIOs) were also accelerated under FT. But the mutual influences of pathogenic bacterial survival and MIOs under FT have not been profoundly explored yet. In this work, aqueous systems containing Escherichia coli as well as synthetic ferrihydrite (Fh) and manganese dioxide (MnO2) were experimented under simulated FT cycles to study the mutual influences of metal oxides and bacteria survival while oxide dissolutions and appearances, bacterial morphology and activities (survival number, cell surface hydrophobicity (CSH) and superoxide dismutase (SOD)) were obtained. The results showed that broken E. coli cells by ice growth were observed, but both oxides promoted E. coli survival under FT stress and prolonged bacterial survival time by 1.2-2.9 times, which were mainly attributed to the release of Fe3+ and Mn2+ caused by FT. The dissolutions of Fh and MnO2 under FT, which took place at a low level in absence of E. coli cells, were markedly enhanced with bacterial interferences by 2-8 times and higher dissolved manganese concentrations were detected than iron. This was probably because that concentrated organic matters which were released from broken cells, rejected into unfrozen liquid layer and acted as electron donors and ligands to oxide dissolution. Compared with Fh system, more significant promotion of E. coli survival under FT in MnO2 systems were found because of more SOD generations associated with high dissolved manganese concentrations and the stronger cellular protection by MnO2 aggregations. The results suggested that FT significantly influenced the interactions between metal oxides and bacterial in water, resulting to changes in pathogen activity and metal element cycling.

High starter phosphorus fertilization facilitates soil phosphorus turnover by promoting microbial functional interaction in an arable soil.

Microbial phosphorus (P) turnover is critical in C utilization efficiency in agroecosystems. It is therefore necessary to understand the P mobilization processes occurring during P fertilization in order to ensure both crop yield and environmental quality. Here, we established a controlled pot experiment containing soil amended with three different levels of starter P fertilizer and collected soil samples after 30, 60, and 90 days of incubation. Quantitative microbial element cycling (QMEC) smart chip technology and 16S rRNA gene sequencing were used to investigate functional gene structures involved in carbon, nitrogen and P cycling and the bacterial community composition of the collected samples. Although P fertilization did not significantly affect the structure of the soil microbial community, some rare microbiota were changed in particular phosphorus-solubilizing bacteria were enriched at the high P fertilization level, suggesting that the rare taxa make an important contribution to P turnover. P fertilization also altered the functional gene structure, and high P concentrations enhanced the functional gene diversity and abundance. Partial redundancy analysis further revealed that changes in rare taxa and functional genes of soil microorganisms drive the alteration of soil P pools. These findings extend our understanding of the microbial mechanisms of P turnover.

Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment.

Hydrothermal vents release reduced compounds and small organic carbon compounds into the surrounding seawater, providing essential substrates for microbial growth and bioenergy transformations. Despite the wide distribution of the marine benthic group E archaea (referred to as Hydrothermarchaeota) in the hydrothermal environment, little is known about their genomic repertoires and biogeochemical significance. Here, we studied four highly complete (>80%) metagenome-assembled genomes (MAGs) from a black smoker chimney and the surrounding sulfur-rich sediments on the South Atlantic Mid-Ocean Ridge and publicly available data sets (the Integrated Microbial Genomes system of the U.S. Department of Energy-Joint Genome Institute and NCBI SRA data sets). Genomic analysis suggested a wide carbon metabolic diversity of Hydrothermarchaeota members, including the utilization of proteins, lactate, and acetate; the anaerobic degradation of aromatics; the oxidation of C1 compounds (CO, formate, and formaldehyde); the utilization of methyl compounds; CO2 incorporation by the tetrahydromethanopterin-based Wood-Ljungdahl pathway; and participation in the type III ribulose-1,5-bisphosphate carboxylase/oxygenase-based Calvin-Benson-Bassham cycle. These microbes also potentially oxidize sulfur, arsenic, and hydrogen and engage in anaerobic respiration based on sulfate reduction and denitrification. Among the 140 MAGs reconstructed from the black smoker chimney microbial community (including Hydrothermarchaeota MAGs), community-level metabolic predictions suggested a redundancy of carbon utilization and element cycling functions and interactive syntrophic and sequential utilization of substrates. These processes might make various carbon and energy sources widely accessible to the microorganisms. Further, the analysis suggested that Hydrothermarchaeota members contained important functional components obtained from the community via lateral gene transfer, becoming a distinctive clade. This might serve as a niche-adaptive strategy for metabolizing heavy metals, C1 compounds, and reduced sulfur compounds. Collectively, the analysis provides comprehensive metabolic insights into the Hydrothermarchaeota IMPORTANCE This study provides comprehensive metabolic insights into the Hydrothermarchaeota from comparative genomics, evolution, and community-level perspectives. Members of the Hydrothermarchaeota synergistically participate in a wide range of carbon-utilizing and element cycling processes with other microorganisms in the community. We expand the current understanding of community interactions within the hydrothermal sediment and chimney, suggesting that microbial interactions based on sequential substrate metabolism are essential to nutrient and element cycling.

Microbial Taxon-Specific Isotope Incorporation with DNA Quantitative Stable Isotope Probing.

Quantitative stable isotope probing (qSIP) measures rates of taxon-specific element assimilation in intact microbial communities, utilizing substrates labeled with a heavy isotope.The laboratory protocol for qSIP is nearly identical to that for conventional stable isotope probing, with two key additions: (1) in qSIP, qPCR measurements are conducted on each density fraction recovered after isopycnic separation, and (2) in qSIP, multiple density fractions are sequenced spanning the entire range of densities over which nucleic acids were recovered. qSIP goes beyond identifying taxa assimilating a substrate, as it also allows for measuring that assimilation for each taxon within a given microbial community. Here, we describe an analysis process necessary to determine atom fraction excess of a heavy stable isotope added to an environmental sample for a given taxon's DNA.