Search

Net nitrogen mineralization (Nmin) and nitrification regulate soil N availability and loss after severe wildfires in boreal forests experiencing slow vegetation recovery. Yet, how microorganisms respond to postfire phosphorus (P) enrichment to alter soil N transformations remains unclear in N-limited boreal forests. Here, we investigated postfire N-P interactions using an intensive regional-scale sampling of 17 boreal forests in the Greater Khingan Mountains (Inner Mongolia-China), a laboratory P-addition incubation, and a continental-scale meta-analysis. We found that postfire soils had an increased risk of N loss by accelerated Nmin and nitrification along with low plant N demand, especially during the early vegetation recovery period. The postfire N/P imbalance created by P enrichment acts as a "N retention" strategy by inhibiting Nmin but not nitrification in boreal forests. This strategy is attributed to enhanced microbial N-use efficiency and N immobilization. Importantly, our meta-analysis found that there was a greater risk of N loss in boreal forest soils after fires than in other climatic zones, which was consistent with our results from the 17 soils in the Greater Khingan Mountains. These findings demonstrate that postfire N-P interactions play an essential role in mitigating N limitation and maintaining nutrient balance in boreal forests.

The co-occurrence of cadmium (Cd) pollution and selenium (Se) deficiency commonly exists in global soils, especially in China. As a result, there is great interest in developing practical agronomic strategies to simultaneously achieve Cd remediation and Se mobilization in paddy soils, thereby enhancing food quality/safety. To this end, we conducted a field-plot trial on soils having high geological background levels of Cd (0.67 mg kg-1) and Se (0.50 mg kg-1). We explored 12 contrasting fertilizers (urea, potassium sulfate (K2SO4), calcium-magnesium-phosphate (CMP)), amendments (manure and biochar) and their combinations on Cd/Se bioavailability. Soil pH, total organic carbon (TOC), soil available Cd/Se, Cd/Se fractions and Cd/Se accumulation in different rice components were determined. No significant differences existed in mean grain yield among treatments. Results showed that application of urea and K2SO4 decreased soil pH, whereas the CMP fertilizer and biochar treatments increased soil pH. There were no significant changes in TOC concentrations. Three treatments (CMP, manure, biochar) significantly decreased soil available Cd, whereas no treatment affected soil available Se at the maturity stage. Four treatments (CMP, manure, biochar and manure＋urea＋CMP＋K2SO4) achieved our dual goal of Cd reduction and Se enrichment in rice grain. Structural equation modeling (SEM) demonstrated that soil available Cd and root Cd were negatively affected by pH and organic matter (OM), whereas soil available Se was positively affected by pH. Moreover, redundancy analysis (RDA) showed strong positive correlations between soil available Cd, exchangeable Cd and reducible Cd with grain Cd concentration, as well as between pH and soil available Se with grain Se concentration. Further, there was a strong negative correlation between residual Cd/Se (non-available fraction) and grain Cd/Se concentrations. Overall, this study identified the primary factors affecting Cd/Se bioavailability, thereby providing new guidance for achieving safe production of Se-enriched rice through fertilizer/amendment management of Cd-enriched soils.

Viruses are crucial in shaping soil microbial functions and ecosystems. However, studies on soil viromes have been limited in both spatial scale and biome coverage. Here we present a comprehensive synthesis of soil virome biogeographic patterns using the Global Soil Virome dataset (GSV) wherein we analysed 1,824 soil metagenomes worldwide, uncovering 80,750 partial genomes of DNA viruses, 96.7% of which are taxonomically unassigned. The biogeography of soil viral diversity and community structure varies across different biomes. Interestingly, the diversity of viruses does not align with microbial diversity and contrasts with it by showing low diversity in forest and shrubland soils. Soil texture and moisture conditions are further corroborated as key factors affecting diversity by our predicted soil viral diversity atlas, revealing higher diversity in humid and subhumid regions. In addition, the binomial degree distribution pattern suggests a random co-occurrence pattern of soil viruses. These findings are essential for elucidating soil viral ecology and for the comprehensive incorporation of viruses into soil ecosystem models.

Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservo)ir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 soil metagenomes. We identify 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome's functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8545 CRISPR-Cas genes. Additionally, we determine that uSGBs contributed 84.6% of previously unexplored viral-host associations from the SMAG catalogue. The SMAG catalogue provides an useful genomic resource for further studies investigating soil microbial biodiversity and genetic resources.

Abstract: Antibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in the spread of antibiotic resistance genes (ARGs) through horizontal gene transfer. Although the occurrence, distribution, and driving factors of ARGs in soils have been widely investigated, little is known about the antibiotic resistance of soilborne pathogens at a global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembled, yielding 407 ARG‐carrying pathogens (APs) with at least one ARG; APs are detected in 1443 samples (sample detection rate of 87.8%). The richness of APs is greater in agricultural soils (with a median of 20) than in non‐agricultural ecosystems. Agricultural soils possess a high prevalence of clinical APs affiliated with Escherichia, Enterobacter, Streptococcus, and Enterococcus. The APs detected in agricultural soils tend to coexist with multidrug resistance genes and bacA. A global map of soil AP richness is generated, where anthropogenic and climatic factors explained AP hot spots in East Asia, South Asia, and the eastern United States. The results herein advance this understanding of the global distribution of soil APs and determine regions prioritized to control soilborne APs worldwide.

The soil microbial food web plays a vital role in soil health, nutrient cycling and agricultural productivity. Notably, there is a distinct paucity of information regarding the effects of heavy metal contamination on trophic-level interactions within the microbial food web of agricultural soils, which experience appreciably metal contamination worldwide. Herein, we investigated trophic interactions among predators (protists), their preys (bacteria and fungi) and competitors (nematodes) under four metal contamination levels using high-throughput sequencing and a laboratory verification experiment. Metal contamination decreased growth of protist-preferential prey (e.g., small-sized and gram-negative bacteria), increased the growth of protist-nonpreferential prey (e.g., pathogenic fungi and Actinobacteria), and had a limited effect on the soil protist-competitor (i.e., nematodes). This resulted in a considerable decrease in the diversity and abundance of protistan consumers and a re-arrangement of their interactions with other organisms. From a systemic view, the direct link was weaker between heavy metal contamination and the protist community than the indirect linkage, i.e., metal-induced changes in the prey community. We further validated these results with laboratory incubation trials that documented growth inhibition of protist (Colpoda) and protist-preferential prey (Spingomonas) versus growth stimulation of protist-nonpreferential prey (Arthrobacter) under metal contamination. These findings indicate that metal contamination collapses trophic-level interactions within the soil microbial food web via bottom-up regulation, providing important implications for managing trophic interactions to maintain agricultural ecosystem services under the challenge of worldwide metal contamination.

Viruses are critical for regulating microbial communities and biogeochemical processes affecting carbon/nutrient cycling. However, the role of soil phages in controlling microbial physiological traits and intrinsic dissolved organic matter (DOM) properties remains largely unknown. Herein, microcosm experiments with different soil phage concentrates (including no-added phages, inactive phages, and three dilutions of active phages) at two temperatures (15 °C and 25 °C) were conducted to disclose the nutrient and DOM dynamics associated with viral lysing. Results demonstrated three different phases of viral impacts on CO2 emission at both temperatures, and phages played a role in maintaining Q10 within bounds. At both temperatures, microbial nutrient limitations (especially P limitation) were alleviated by viral lysing as determined by extracellular enzyme activity (decreased Vangle with active phages). Additionally, the re-utilization of lysate-derived DOM by surviving microbes stimulated an increase of microbial metabolic efficiency and recalcitrant DOM components (e.g., SUV254, SUV260 and HIX). This research provides direct experimental evidence that the "viral shuttle" exists in soils, whereby soil phages increase recalcitrant DOM components. Our findings advance the understanding of viral controls on soil biogeochemical processes, and provide a new perspective for assessing whether soil phages provide a net "carbon sink" vs. "carbon source" in soils.

The response of soil microbes to heavy metal pollution provides a metric to evaluate the soil health and ecological risks associated with heavy metal contamination. However, a multitrophic level perspective of how soil microbial communities and their functions respond to long-term exposure of multiple heavy metals remains unclear. Herein, we examined variations in soil microbial (including protists and bacteria) diversity, functional guilds and interactions along a pronounced metal pollution gradient in a field surrounding an abandoned electroplating factory. Given the stressful soil environment resulting from extremely high heavy metal concentrations and low nutrients, beta diversity of protist increased, but that of bacteria decreased, at high versus low pollution sites. Additionally, the bacteria community showed low functional diversity and redundancy at the highly polluted sites. We further identified indicative genus and "generalists" in response to heavy metal pollution. Predatory protists in Cercozoa were the most sensitive protist taxa with respect to heavy metal pollution, whereas photosynthetic protists showed a tolerance for metal pollution and nutrient deficiency. The complexity of ecological networks increased, but the communication among the modules disappeared with increasing metal pollution levels. Subnetworks of tolerant bacteria displaying functional versatility (Blastococcus, Agromyces and Opitutus) and photosynthetic protists (microalgae) became more complex with increasing metal pollution levels, indicating their potential for use in bioremediation and restoration of abandoned industrial sites contaminated by heavy metals.

Abstract: Background: The rRNA operon (rrn) copy number is associated with protein synthesis and reproduction, reflecting microbial r- and K-life strategies and influencing soil ecosystem function. Although the positive relationship between microbial community-level rrn copy numbers and nutrient availability has been reported, the association between rrn copy number and soil stoichiometry or environmental stress remains largely unknown, particularly in the context of long-term nutrient inputs.Results: Using long-term (> 30 years) field experiments across three agro-ecosystems, we consistently found that N fertilization increased the microbial community-level rrn copy number. This increase was equivalently explained by soil CN stoichiometry (22%) and soil acidification (21%). Balanced soil CN stoichiometry favored the growth of N-dependent copiotrophs such as Bacilliand Flavobacteriia containing high rrn copy numbers (an average of 2.5), and enhanced their nutrient competition ability. Moreover, N fertilization-induced soil acidification, as an environmental stressor, increased the abundance of pH-negative responders such as Clostridia and Ktedonobacteria which also contained high rrn copy numbers (2.8), and threatened rare taxa with low rrn copy numbers.Conclusions: Consequently, our finding challenges the concept of microbial life-strategy regulation solely by nutrient availability, highlighting the novelty of significant contributions of soil stoichiometric balance and environmental stress to microbial strategies in agro-ecosystems under long-term nutrient inputs.

Water pollution is a great risk to aquatic ecosystems and human health. Among water pollution remediation strategies, adsorption mechanisms provide strong efficacy for a wide variety of pollutants. Several recent efforts examined the development of low cost adsorbents utilizing commonly available agricultural wastes. However, raw (i.e., unaltered) agricultural wastes typically exhibit low sorption capacity for pollutants due to their non-reactive structural/composition properties. Hence, modifications of raw agricultural wastes to enhance their sorption capacities for various aquatic pollutants are necessary to optimize their performance for pollutant removal. Numerous modification techniques are effective in altering agricultural wastes for improved sorption performance. This paper reviews the development of modified agricultural waste materials for pollutant removal from water. We compiled an extensive inventory of modification techniques applied to agricultural wastes to enhance their adsorption capacities for removal of a wide range of pollutants. Modification strategies and their effects on sorption properties were rigorously examined to highlight key advancements in the preparation of adsorbents from agricultural wastes. Finally, the costs of these materials were examined, along with the benefits and drawbacks concerning their use. This review provides a thorough assessment for advancing the utilization of agricultural wastes for preparing adsorbents for water treatment. Graphical Abstract: [Figure not available: see fulltext.]

Arsenic (As) is the most ubiquitous toxic metalloid in nature. Microbe-mediated As metabolism plays an important role in global As biogeochemical processes, greatly changing its toxicity and bioavailability. While metagenomic sequencing may advance our understanding of the As metabolism capacity of microbial communities in different environments, accurate metagenomic profiling of As metabolism remains challenging due to low coverage and inaccurate definitions of As metabolism gene families in public orthology databases. Here we developed a manually curated As metabolism gene database (AsgeneDB) comprising 400 242 representative sequences from 59 As metabolism gene families, which are affiliated with 1653 microbial genera from 46 phyla. AsgeneDB achieved 100% annotation sensitivity and 99.96% annotation accuracy for an artificial gene dataset. We then applied AsgeneDB for functional and taxonomic profiling of As metabolism in metagenomes from various habitats (freshwater, hot spring, marine sediment and soil). The results showed that AsgeneDB substantially improved the mapping ratio of short reads in metagenomes from various environments. Compared with other databases, AsgeneDB provides more accurate, more comprehensive and faster analysis of As metabolic genes. In addition, we developed an R package, Asgene, to facilitate the analysis of metagenome sequencing data. Therefore, AsgeneDB and the associated Asgene package will greatly promote the study of As metabolism in microbial communities in various environments.