Community proteogenomics reveals the systemic impact of phosphorus availability on microbial functions in tropical soil

Rare taxa mediate microbial carbon and nutrient limitation in the rhizosphere and bulk soil under sugarcane-peanut intercropping systems

Introduction

Microbial carbon (C) and nutrient limitation exert key influences on soil organic carbon (SOC) and nutrient cycling through enzyme production for C and nutrient acquisition. However, the intercropping effects on microbial C and nutrient limitation and its driving factors between rhizosphere and bulk soil are unclear.

Methods

Therefore, we conducted a field experiment that covered sugarcane-peanut intercropping with sole sugarcane and peanut as controls and to explore microbial C and nutrient limitation based on the vector analysis of enzyme stoichiometry; in addition, microbial diversity was investigated in the rhizosphere and bulk soil. High throughput sequencing was used to analyze soil bacterial and fungal diversity through the 16S rRNA gene and internal transcribed spacer (ITS) gene at a phylum level.

Results

Our results showed that sugarcane-peanut intercropping alleviated microbial C limitation in all soils, whereas enhanced microbial phosphorus (P) limitation solely in bulk soil. Microbial P limitation was also stronger in the rhizosphere than in bulk soil. These results revealed that sugarcane-peanut intercropping and rhizosphere promoted soil P decomposition and facilitated soil nutrient cycles. The Pearson correlation results showed that microbial C limitation was primarily correlated with fungal diversity and fungal rare taxa (Rozellomycota, Chyltridiomycota, and Calcarisporiellomycota) in rhizosphere soil and was correlated with bacterial diversity and most rare taxa in bulk soil. Microbial P limitation was solely related to rare taxa (Patescibacteria and Glomeromycota) in rhizosphere soil and related to microbial diversity and most rare taxa in bulk soil. The variation partitioning analysis further indicated that microbial C and P limitation was explained by rare taxa (7%-35%) and the interactions of rare and abundant taxa (65%-93%).

Conclusion

This study indicated the different intercropping effects on microbial C and nutrient limitation in the rhizosphere and bulk soil and emphasized the importance of microbial diversity, particularly rare taxa.

Soil microbial functional profiles of P-cycling reveal drought-induced constraints on P-transformation in a hyper-arid desert ecosystem

Soil water conditions are known to influence soil nutrient availability, but the specific impact of different conditions on soil phosphorus (P) availability through the modulation of P-cycling functional microbial communities in hyper-arid desert ecosystems remains largely unexplored. To address this knowledge gap, we conducted a 3-year pot experiment using a typical desert plant species (Alhagi sparsifolia Shap.) subjected to two water supply levels (25 %-35 % and 65 %-75 % of maximum field capacity, MFC) and four P-supply levels (0, 1, 3, and 5 g P m-2 y-1). Our investigation focused on the soil Hedley-P pool and the four major microbial groups involved in the critical phases of soil microbial P-cycling. The results revealed that the drought (25 %-35 % MFC) and no P-supply treatments reduced soil resin-P and NaHCO3-Pi concentrations by 87.03 % and 93.22 %, respectively, compared to the well-watered (65 %-75 % MFC) and high P-supply (5 g P m-2 y-1) treatments. However, the P-supply treatment resulted in a 12 %-22 % decrease in the soil NH4+-N concentration preferred by microbes compared to the no P-supply treatment. Moreover, the abundance of genes engaged in microbial P-cycling (e.g. gcd and phoD) increased under the drought and no P-supply treatments (p < 0.05), suggesting that increased NH4+-N accumulation under these conditions may stimulate P-solubilizing microbes, thereby promoting the microbial community's investment in resources to enhance the P-cycling potential. Furthermore, the communities of Steroidobacter cummioxidans, Mesorhizobium alhagi, Devosia geojensis, and Ensifer sojae, associated with the major P-cycling genes, were enriched in drought and no or low-P soils. Overall, the drought and no or low-P treatments stimulated microbial communities and gene abundances involved in P-cycling. However, this increase was insufficient to maintain soil P-bioavailability. These findings shed light on the responses and feedback of microbial-mediated P-cycling behaviors in desert ecosystems under three-year drought and soil P-deficiency.

Deforestation impacts soil biodiversity and ecosystem services worldwide

Deforestation poses a global threat to biodiversity and its capacity to deliver ecosystem services. Yet, the impacts of deforestation on soil biodiversity and its associated ecosystem services remain virtually unknown. We generated a global dataset including 696 paired-site observations to investigate how native forest conversion to other land uses affects soil properties, biodiversity, and functions associated with the delivery of multiple ecosystem services. The conversion of native forests to plantations, grasslands, and croplands resulted in higher bacterial diversity and more homogeneous fungal communities dominated by pathogens and with a lower abundance of symbionts. Such conversions also resulted in significant reductions in carbon storage, nutrient cycling, and soil functional rates related to organic matter decomposition. Responses of the microbial community to deforestation, including bacterial and fungal diversity and fungal guilds, were predominantly regulated by changes in soil pH and total phosphorus. Moreover, we found that soil fungal diversity and functioning in warmer and wetter native forests is especially vulnerable to deforestation. Our work highlights that the loss of native forests to managed ecosystems poses a major global threat to the biodiversity and functioning of soils and their capacity to deliver ecosystem services.

Alleviating the adverse effects of Cd-Pb contamination through the application of silicon fertilizer: Enhancing soil microbial diversity and mitigating heavy metal contamination

The use of silicon fertilizer (SF) as a means of remediating cadmium (Cd) and lead (Pb) pollution has proven to be beneficial. However, the mechanism via which SF enhances soil quality and crop productivity under Cd- and Pb-contaminated soil (S) remains unclear. This study investigated the impacts of chemical fertilizer, mineral SF (MSF), and organic SF (OSF) on microbial community structure, activity of nutrient acquisition enzymes, and growth of tobacco in the presence of S condition. SF significantly reduced the contents of Cd and Pb in soil under S condition by 6.92-42.43% and increased plant height and leaf area by 15.27-81.77%. Moreover, the use of SF was observed to increase the efficiency of soil carbon and phosphorus cycling under S condition by 6.88-23.08%. Concurrently, SF was found to play a crucial role in facilitating the establishment of a complex, efficient, and interdependent molecular ecological network among soil microorganisms. In this context, Actinobacteriota, Bacteroidota, Ascomycota, and Basidiomycota were observed to be integral components of this network. SF was found to have a substantial positive impact on the metabolic functions and organismal systems of soil microorganisms. Moreover, the combined utilization of the Mantel test and partial least squares path model provided empirical evidence supporting the assertion that the administration of SF had a positive impact on both soil nutrient acquisition enzyme activity and tobacco growth, which was attributed to the enhancement of soil microbial diversity resulting from the application of SF. Furthermore, compared with MSF, OSF has advantages in reducing soil Pb and Cd content, promoting tobacco agronomic traits, increasing the number of key microbial communities, and maintaining the structural stability of microbial networks. The aforementioned findings, therefore, suggest that the OSF played a pivotal role in alleviating the adverse impacts of S, thereby demonstrating its efficacy in this particular process.

Effects of temperature-related changes on charred bone in soil: From P release to microbial community

Phosphorus (P) is one of the most common limited nutrients in terrestrial ecosystems. Animal bones, with abundant bioapatite, are considerable P sources in terrestrial ecosystems. Heating significantly promotes P release from bone bioapatite, which may alleviate P limitation in soil. This study aimed to explore P release from charred bone (CB) under heating at various temperatures (based on common natural heating). It showed that heating at ∼300 °C significantly increased the P release (up to ∼30 mg/kg) from CB compared with other heating temperatures. Then, the subsequent changes of available P and pH induced evident alternation of soil microbial community composition. For instance, CB heated at ∼300 °C caused elevation of phosphate-solubilizing fungi (PSF) abundance. This further stimulated P mobility in the soil. Meanwhile, the fungal community assembly process was shifted from stochastic to deterministic, whereas the bacterial community was relatively stable. This indicated that the bacterial community showed fewer sensitive responses to the CB addition. This study hence elucidated the significant contribution of heated bone materials on P supply. Moreover, functional fungi might assist CB treated by natural heating (e.g., fire) to construct P "Hot Spots".

Understanding how various forms of phosphorus stress affect microbiome functions and boost plant disease resistance: Insights from metagenomic analysis

The plant's response to phosphorus (P) starvation suppresses its immunity and regulates rhizosphere microbial colonization. However, the impact of various P forms on plant disease resistance and microbial composition remains underreported. This paper examines the soybean rhizosphere microbiome facing co-stress from Fusarium oxysporum and diverse P forms. Macrogenomic analysis evaluates whether P addition enhances plant disease resistance and rhizosphere microbial function, and if such effects relate to P forms. Results show that different P forms mitigate F. oxysporum-induced plant inhibition by promoting P turnover. P forms predominantly affect microbial composition, followed by soil and plant properties. In soybean, the phosphate transport strategy (ugpA/Q) was selected to maintain high P to enhance immunity in the KH2PO4 treatment, while organo-P mineralization (phnH/F/W/G) was selected for superphosphate treatment. The Frankiales, a P-turnover microorganism, copiotrophic microorganisms, and indicator bacteria of plant properties, initially increase after F. oxysporum inoculation and then decrease post P addition, regardless of P forms. Additionally, the rhizosphere microbial community's metabolic activities and compounds significantly aid soybean defense against F. oxysporum, with functional types depending on P forms. Therefore, these findings establish a novel approach to enhance host defense against soil-borne diseases through P nutrition regulation to mediate host-driven metabolic activities of microbial communities.

Proteogenomics-based functional genome research: approaches, applications, and perspectives in plants

Proteogenomics (PG) integrates the proteome with the genome and transcriptome to refine gene models and annotation. Coupled with single-cell (SC) assays, PG effectively distinguishes heterogeneity among cell groups. Affiliating spatial information to PG reveals the high-resolution circuitry within SC atlases. Additionally, PG can investigate dynamic changes in protein-coding genes in plants across growth and development as well as stress and external stimulation, significantly contributing to the functional genome. Here we summarize existing PG research in plants and introduce the technical features of various methods. Combining PG with other omics, such as metabolomics and peptidomics, can offer even deeper insights into gene functions. We argue that the application of PG will represent an important font of foundational knowledge for plants.

Conversion of steppe to cropland increases spatial heterogeneity of soil functional genes

The microbiome function responses to land use change are important for the long-term prediction and management of soil ecological functions under human influence. However, it has remains uncertain how the biogeographic patterns of soil functional composition change when transitioning from natural steppe soils (NS) to agricultural soils (AS). We collected soil samples from adjacent pairs of AS and NS across 900 km of Mollisol areas in northeast China, and the soil functional composition was characterized using shotgun sequencing. AS had higher functional alpha-diversity indices with respect to KO trait richness and a higher Shannon index than NS. The distance-decay slopes of functional gene composition were steeper in AS than in NS along both spatial and environmental gradients. Land-use conversion from steppe to farmland diversified functional gene profiles both locally and spatially; it increased the abundances of functional genes related to labile carbon, but decreased those related to recalcitrant substrate mobilization (e.g., lignin), P cycling, and S cycling. The composition of gene functional traits was strongly driven by stochastic processes, while the degree of stochasticity was higher in NS than in AS, as revealed by the neutral community model and normalized stochasticity ratio analysis. Alpha-diversity of core functional genes was strongly related to multi-nutrient cycling in AS, suggesting a key relationship to soil fertility. The results of this study challenge the paradigm that the conversion of natural to agricultural habitat will homogenize soil properties and biology while reducing local and regional gene functional diversity.

Microbial communities in terrestrial surface soils are not widely limited by carbon

Microbial communities in soils are generally considered to be limited by carbon (C), which could be a crucial control for basic soil functions and responses of microbial heterotrophic metabolism to climate change. However, global soil microbial C limitation (MCL) has rarely been estimated and is poorly understood. Here, we predicted MCL, defined as limited availability of substrate C relative to nitrogen and/or phosphorus to meet microbial metabolic requirements, based on the thresholds of extracellular enzyme activity across 847 sites (2476 observations) representing global natural ecosystems. Results showed that only about 22% of global sites in terrestrial surface soils show relative C limitation in microbial community. This finding challenges the conventional hypothesis of ubiquitous C limitation for soil microbial metabolism. The limited geographic extent of C limitation in our study was mainly attributed to plant litter, rather than soil organic matter that has been processed by microbes, serving as the dominant C source for microbial acquisition. We also identified a significant latitudinal pattern of predicted MCL with larger C limitation at mid- to high latitudes, whereas this limitation was generally absent in the tropics. Moreover, MCL significantly constrained the rates of soil heterotrophic respiration, suggesting a potentially larger relative increase in respiration at mid- to high latitudes than low latitudes, if climate change increases primary productivity that alleviates MCL at higher latitudes. Our study provides the first global estimates of MCL, advancing our understanding of terrestrial C cycling and microbial metabolic feedback under global climate change.

Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils

Microorganisms play crucial roles in phosphorus (P) turnover and P bioavailability increases in heavy metal-contaminated soils. However, microbially driven P-cycling processes and mechanisms of their resistance to heavy metal contaminants remain poorly understood. Here, we examined the possible survival strategies of P-cycling microorganisms in horizontal and vertical soil samples from the world's largest antimony (Sb) mining site, which is located in Xikuangshan, China. We found that total soil Sb and pH were the primary factors affecting bacterial community diversity, structure and P-cycling traits. Bacteria with the gcd gene, encoding an enzyme responsible for gluconic acid production, largely correlated with inorganic phosphate (Pi) solubilization and significantly enhanced soil P bioavailability. Among the 106 nearly complete bacterial metagenome-assembled genomes (MAGs) recovered, 60.4% carried the gcd gene. Pi transportation systems encoded by pit or pstSCAB were widely present in gcd-harboring bacteria, and 43.8% of the gcd-harboring bacteria also carried the acr3 gene encoding an Sb efflux pump. Phylogenetic and potential horizontal gene transfer (HGT) analyses of acr3 indicated that Sb efflux could be a dominant resistance mechanism, and two gcd-harboring MAGs appeared to acquire acr3 through HGT. The results indicated that Sb efflux could enhance P cycling and heavy metal resistance in Pi-solubilizing bacteria in mining soils. This study provides novel strategies for managing and remediating heavy metal-contaminated ecosystems.

Metagenomics reveals the effect of long-term fertilization on carbon cycle in the maize rhizosphere

Long-term fertilization can result in the changes in carbon (C) cycle in the maize rhizosphere soil. However, there have been few reports on the impacts of microbial regulatory mechanisms on the C cycle in soil. In the study, we analyzed the response of functional genes that regulate the C fixation, decomposition and methane (CH₄) metabolism in maize rhizosphere soil to different fertilization treatments using metagenomics analysis. As the dominant C fixation pathway in maize rhizosphere soil, the abundance of the functional genes regulating the reductive citrate cycle (rTCA cycle) including korA, korB, and IHD1 was higher under the chemical nitrogen (N) fertilizer treatments [nitrogen fertilizer (N), compound chemical fertilization (NPK), the combination of compound chemical fertilizer with maize straw (NPKS)] than maize straw return treatments [maize straw return (S), the combination of phosphorus and potassium fertilizer with maize straw (PKS)]. The NPK treatment decreased the abundance of functional genes involved in 3-hydroxypropionate bicycle (3-HP cycle; porA, porB, and porD), which was one of the major C fixation pathways in soil aside from dicarboxylate-hydroxybutyrate (DC/4-HB cycle) and Calvin cycle. The abundance of functional genes related to C degradation was higher in S, PKS and NPKS treatments than N and NPK treatments, and chemical N fertilizer application had a significant effect on C degradation. The dominant Methanaogenesis pathway in maize rhizosphere soil, used acetate as a substrate, and was significantly promoted under chemical N fertilizer application. The functional genes that were related to CH₄ oxidation (i.e., pmoA and pmoB) were reduced under N and NPK treatments. Moreover, soil chemical properties had a significant impact on the functional genes related to C fixation and degradation, with SOC (r² = 0.79) and NO₃^--N (r² = 0.63) being the main regulators. These results implied that N fertilization rather than maize straw return had a greater influence on the C cycle in maize rhizosphere soil.

Abundant bacterial subcommunity is structured by a stochastic process in an agricultural system with P fertilizer inputs

Soil microorganisms play an important role in agroecosystems and are related to ecosystem functioning. Nevertheless, little is understood about their community assembly and the major factors regulating stochastic and deterministic processes, particularly with respect to the comparison of abundant and rare bacterial subcommunities in agricultural systems. Here, we investigated the assembly of abundant and rare bacterial subcommunities in fields with different crops (maize and wheat) and phosphorus (P) fertilizer input at three different growth stages on the Loess Plateau. The high-throughput sequencing dataset was assessed using null and neutral community models. We found that abundant bacteria was governed by the stochastic process of homogenizing dispersal, but rare bacterial subcommunity was predominant by deterministic processes in maize and wheat fields due to broader niche breadths of abundant species. Soil nitrogen (N) and P also determined the assembly of abundant and rare soil subcommunities. The relative abundance and composition of the abundant and rare bacterial subcommunities were also influenced by soil nutrients (soil available P (AP) and NO₃^--N) and agricultural practices (P fertilization and crop cultivation). In addition, the abundant bacterial community was more susceptible to P fertilizer input than that of the rare bacteria, and a higher relative abundance of abundant bacteria was observed in the P70 treatment both in maize and wheat soils. The microbial co-occurrence network analysis indicated that the maize field and low nutrient treatment exhibited stronger associations and that the abundant bacteria showed fewer interconnections. This study provides new insights toward understanding the mechanisms for the assembly of abundant and rare bacterial taxa in dryland cropping systems, enhancing our understanding of ecosystem diversity theory in microbial ecology.

Long-term phosphorus addition alleviates CO2 and N2O emissions via altering soil microbial functions in secondary rather primary tropical forests

Tropical forests, where the soils are nitrogen (N) rich but phosphorus (P) poor, have a disproportionate influence on global carbon (C) and N cycling. While N deposition substantially alters soil C and N retention in tropical forests, whether P input can alleviate these N-induced effects by regulating soil microbial functions remains unclear. We investigated soil microbial taxonomy and functional traits in response to 10-year independent and interactive effects of N and P additions in a primary and a secondary tropical forest in Hainan Island. In the primary forest, N addition boosted oligotrophic bacteria and phosphatase and enriched genes responsible for C-, P-mineralization, nitrification and denitrification, suggesting aggravated P limitation while N excess. This might stimulate P excavation via organic matter mineralization, and enhance N losses, thereby increasing soil CO₂ and N₂O emissions by 86% and 110%, respectively. Phosphorus and NP additions elevated C-mining enzymes activity mainly due to intensified C limitation, causing 82% increase in CO₂ emission. In secondary forest, P and NP additions reduced phosphatase activity, enriched fungal copiotrophs and increased microbial biomass, suggesting removal of nutrient deficiencies and stimulation of fungal growth. Meanwhile, soil CO₂ emission decreased by 25% and N₂O emission declined by 52-82% due to alleviated P acquisition from organic matter decomposition and increased microbial C and N immobilization. Overall, N addition accelerates most microbial processes for C and N release in tropical forests. Long-term P addition increases C and N retention via reducing soil CO₂ and N₂O emissions in the secondary but not primary forest because of strong C limitation to microbial N immobilization. Further, the seasonal and annual variations in CO₂ and N₂O emissions should be considered in future studies to test the generalization of these findings and predict and model dynamics in greenhouse gas emissions and C and N cycling.

Roles of phosphate-solubilizing bacteria in mediating soil legacy phosphorus availability

Phosphorus (P), an essential macronutrient for all life on Earth, has been shown to be a vital limiting nutrient element for plant growth and yield. P deficiency is a common phenomenon in terrestrial ecosystems across the world. Chemical phosphate fertilizer has traditionally been employed to solve the problem of P deficiency in agricultural production, but its application has been limited by the non-renewability of raw materials and the adverse influence on the ecological health of the environment. Therefore, it is imperative to develop efficient, economical, environmentally friendly and highly stable alternative strategies to meet the plant P demand. Phosphate-solubilizing bacteria (PSB) are able to improve plant productivity by increasing P nutrition. Pathways to fully and effectively use PSB to mobilize unavailable forms of soil P for plants has become a hot research topic in the fields of plant nutrition and ecology. Here, the biogeochemical P cycling in soil systems are summarized, how to make full use of soil legacy P via PSB to alleviate the global P resource shortage are reviewed. We highlight the advances in multi-omics technologies that are helpful for exploring the dynamics of nutrient turnover and the genetic potential of PSB-centered microbial communities. Furthermore, the multiple roles of PSB inoculants in sustainable agricultural practices are analyzed. Finally, we project that new ideas and techniques will be continuously infused into fundamental and applied research to achieve a more integrated understanding of the interactive mechanisms of PSB and rhizosphere microbiota/plant to maximize the efficacy of PSB as P activators.

Cross-Feedings, Competition, and Positive and Negative Synergies in a Four-Species Synthetic Community for Anaerobic Degradation of Cellulose to Methane

Complex interactions exist among microorganisms in a community to carry out ecological processes and adapt to changing environments. Here, we constructed a quad-culture consisting of a cellulolytic bacterium (Ruminiclostridium cellulolyticum), a hydrogenotrophic methanogen (Methanospirillum hungatei), an acetoclastic methanogen (Methanosaeta concilii), and a sulfate-reducing bacterium (Desulfovibrio vulgaris). The four microorganisms in the quad-culture cooperated via cross-feeding to produce methane using cellulose as the only carbon source and electron donor. The community metabolism of the quad-culture was compared with those of the R. cellulolyticum-containing tri-cultures, bi-cultures, and mono-culture. Methane production was higher in the quad-culture than the sum of the increases in the tri-cultures, which was attributed to a positive synergy of four species. In contrast, cellulose degradation by the quad-culture was lower than the additive effects of the tri-cultures which represented a negative synergy. The community metabolism of the quad-culture was compared between a control condition and a treatment condition with sulfate addition using metaproteomics and metabolic profiling. Sulfate addition enhanced sulfate reduction and decreased methane and CO₂ productions. The cross-feeding fluxes in the quad-culture in the two conditions were modeled using a community stoichiometric model. Sulfate addition strengthened metabolic handoffs from R. cellulolyticum to M. concilii and D. vulgaris and intensified substrate competition between M. hungatei and D. vulgaris. Overall, this study uncovered emergent properties of higher-order microbial interactions using a four-species synthetic community. IMPORTANCE A synthetic community was designed using four microbial species that together performed distinct key metabolic processes in the anaerobic degradation of cellulose to methane and CO₂. The microorganisms exhibited expected interactions, such as cross-feeding of acetate from a cellulolytic bacterium to an acetoclastic methanogen and competition of H₂ between a sulfate reducing bacterium and a hydrogenotrophic methanogen. This validated our rational design of the interactions between microorganisms based on their metabolic roles. More interestingly, we also found positive and negative synergies as emergent properties of high-order microbial interactions among three or more microorganisms in cocultures. These microbial interactions can be quantitatively measured by adding and removing specific members. A community stoichiometric model was constructed to represent the fluxes in the community metabolic network. This study paved the way toward a more predictive understanding of the impact of environmental perturbations on microbial interactions sustaining geochemically significant processes in natural systems.

Altered microbial P cycling genes drive P availability in soil after afforestation

Soil Phosphorous (P) availability is a limiting factor for plant growth and regulates biological metabolism in plantation ecosystems. The effect of variations in soil microbial P cycling potential on the availability of soil P during succession in plantation ecosystems is unclear. In this study, a metagenomics approach was used to explore variations in the composition and diversity of microbial P genes along a 45-year recovery sequence of Robinia pseudoacacia on the Loess Plateau, as well soil properties were measured. Our results showed that the diversity of P cycling genes (inorganic P solubilization and organic P mineralization genes) increased significantly after afforestation, and the community composition showed clear differences. The gcd and ppx genes were dominant in inorganic P transformation, whereas phnM gene dominated the transformation of organic P. The abundance of genes involved in inorganic P solubilization and organic P mineralization was significantly positively correlated with P availability, particularly for phnM, gcd, ppx, and phnI genes, corresponding to the phyla Gemmatimonadetes, Acidobacteria, Bacteroidetes, and Planctomycetes. The critical drivers of the microbial main genes of soil P cycling were available P (AP) and total N (TN) in soil. Overall, these findings highlight afforestation-induced increases in microbial P cycling genes enhanced soil P availability. and help to better understand how microbial growth metabolism caused by vegetation restoration in ecologically fragile areas affects the soil P cycling.

Climate and edaphic factors drive soil enzyme activity dynamics and tolerance to Cd toxicity after rewetting of dry soil

The intense drying-rewetting cycle due to climate change can affect soil microbial community composition and function, resulting in long-term consequences for belowground carbon and nutrient dynamics. However, how climatic and edaphic factors influence the responses of enzymes to rewetting and their responses to additional perturbation (e.g., heavy metal pollution) after the drying-rewetting history are not well understood. In this study, we collected 18 surface soils from farmlands across various climate zones in China. We chose dehydrogenase (DHA) and alkaline phosphomonoesterase (ALP) as representative intracellular and extracellular enzymes, respectively, and investigated their tolerance to additional perturbation by adding metal ions (i.e., Cd²⁺) upon rewetting. In all soils, rewetting increased DHA activities but did not affect ALP activities compared to air-dried soils. Rewetting increased the tolerances of DHA and ALP to Cd stress, suggesting that the drying-rewetting history may reduce the susceptibility of soil enzymes to additional disturbance. The results demonstrate that differentiating enzymes based on their location in the soil will improve our ability to assess the stress response of microbial communities to drastic fluctuations in soil moisture, thereby better predicting the legacy of climate change on microbial function in soils contaminated with heavy metals.

In-depth characterization of phytase-producing plant growth promotion bacteria isolated in alpine grassland of Qinghai-Tibetan Plateau

The use of plant growth promoting bacteria (PGPB) express phytase (myo-inositol hexakisphosphate phosphohydrolase) capable of hydrolyzing inositol phosphate in soil was a sustainable approach to supply available phosphorus (P) to plants. A total of 73 bacterial isolates with extracellular phytase activity were selected from seven dominant grass species rhizosphere in alpine grassland of Qinghai-Tibetan Plateau. Then, the plant growth promoting (PGP) traits of candidate bacteria were screened by qualitative and quantitative methods, including organic/inorganic Phosphorus solubilization (P. solubilization), plant hormones (PHs) production, nitrogen fixation, 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity and antimicrobial activity. Further experiment were conducted to test their growth promoting effect on Lolium perenne L. under P-limitation. Our results indicated that these bacteria as members of phyla Proteobacteria (90.41%) and Actinobacteria (9.59%) were related to 16 different genera. The isolates of Pseudomonas species showed the highest isolates number (36) and average values of phytase activity (0.267 ± 0.012 U mL^-1), and showed a multiple of PGP traits, which was a great candidate for PGPBs. In addition, six strains were positive in phytase gene (β-propeller phytase, bpp) amplification, which significantly increased the shoot length, shoot/root fresh weight, root average diameter and root system phytase activity of Lolium perenne L. under P-limitation, and the expression of phytase gene (bppP) in root system were verified by qPCR. Finally, the PHY101 gene encoding phytase from Pseudomonas mandelii GS10-1 was cloned, sequenced, and recombinantly expressed in Escherichia coli. Biochemical characterization demonstrated that the recombinant phytase PHY101 revealed the highest activity at pH 6 and 40°C temperature. In particular, more than 60% of activity was retained at a low temperature of 15°C. This study demonstrates the opportunity for commercialization of the phytase-producing PGPB to developing localized microbial inoculants and engineering rhizobacteria for sustainable use in alpine grasslands.

Selectivity in Enzymatic Phosphorus Recycling from Biopolymers: Isotope Effect, Reactivity Kinetics, and Molecular Docking with Fungal and Plant Phosphatases

Among ubiquitous phosphorus (P) reserves in environmental matrices are ribonucleic acid (RNA) and polyphosphate (polyP), which are, respectively, organic and inorganic P-containing biopolymers. Relevant to P recycling from these biopolymers, much remains unknown about the kinetics and mechanisms of different acid phosphatases (APs) secreted by plants and soil microorganisms. Here we investigated RNA and polyP dephosphorylation by two common APs, a plant purple AP (PAP) from sweet potato and a fungal phytase from Aspergillus niger. Trends of δ¹⁸O values in released orthophosphate during each enzyme-catalyzed reaction in ¹⁸O-water implied a different extent of reactivity. Subsequent enzyme kinetics experiments revealed that A. niger phytase had 10-fold higher maximum rate for polyP dephosphorylation than the sweet potato PAP, whereas the sweet potato PAP dephosphorylated RNA at a 6-fold faster rate than A. niger phytase. Both enzymes had up to 3 orders of magnitude lower reactivity for RNA than for polyP. We determined a combined phosphodiesterase-monoesterase mechanism for RNA and terminal phosphatase mechanism for polyP using high-resolution mass spectrometry and ³¹P nuclear magnetic resonance, respectively. Molecular modeling with eight plant and fungal AP structures predicted substrate binding interactions consistent with the relative reactivity kinetics. Our findings implied a hierarchy in enzymatic P recycling from P-polymers by phosphatases from different biological origins, thereby influencing the relatively longer residence time of RNA versus polyP in environmental matrices. This research further sheds light on engineering strategies to enhance enzymatic recycling of biopolymer-derived P, in addition to advancing environmental predictions of this P recycling by plants and microorganisms.

MetaLP: An integrative linear programming method for protein inference in metaproteomics

Metaproteomics based on high-throughput tandem mass spectrometry (MS/MS) plays a crucial role in characterizing microbiome functions. The acquired MS/MS data is searched against a protein sequence database to identify peptides, which are then used to infer a list of proteins present in a metaproteome sample. While the problem of protein inference has been well-studied for proteomics of single organisms, it remains a major challenge for metaproteomics of complex microbial communities because of the large number of degenerate peptides shared among homologous proteins in different organisms. This challenge calls for improved discrimination of true protein identifications from false protein identifications given a set of unique and degenerate peptides identified in metaproteomics. MetaLP was developed here for protein inference in metaproteomics using an integrative linear programming method. Taxonomic abundance information extracted from metagenomics shotgun sequencing or 16s rRNA gene amplicon sequencing, was incorporated as prior information in MetaLP. Benchmarking with mock, human gut, soil, and marine microbial communities demonstrated significantly higher numbers of protein identifications by MetaLP than ProteinLP, PeptideProphet, DeepPep, PIPQ, and Sipros Ensemble. In conclusion, MetaLP could substantially improve protein inference for complex metaproteomes by incorporating taxonomic abundance information in a linear programming model.

A review on effective soil health bio-indicators for ecosystem restoration and sustainability

Preventing degradation, facilitating restoration, and maintaining soil health is fundamental for achieving ecosystem stability and resilience. A healthy soil ecosystem is supported by favorable components in the soil that promote biological productivity and provide ecosystem services. Bio-indicators of soil health are measurable properties that define the biotic components in soil and could potentially be used as a metric in determining soil functionality over a wide range of ecological conditions. However, it has been a challenge to determine effective bio-indicators of soil health due to its temporal and spatial resolutions at ecosystem levels. The objective of this review is to compile a set of effective bio-indicators for developing a better understanding of ecosystem restoration capabilities. It addresses a set of potential bio-indicators including microbial biomass, respiration, enzymatic activity, molecular gene markers, microbial metabolic substances, and microbial community analysis that have been responsive to a wide range of ecosystem functions in agricultural soils, mine deposited soil, heavy metal contaminated soil, desert soil, radioactive polluted soil, pesticide polluted soil, and wetland soils. The importance of ecosystem restoration in the United Nations Sustainable Development Goals was also discussed. This review identifies key management strategies that can help in ecosystem restoration and maintain ecosystem stability.

Nitrogen and phosphorus addition exerted different influences on litter and soil carbon release in a tropical forest

Terrestrial soils release large amount of carbon dioxide (CO₂) each year, which are mainly derived from litter and soil carbon (C) decomposition. Nutrient availability, especially nitrogen (N) and phosphorus (P), plays an important role in both litter and soil C decomposition. Therefore, understanding the underlying mechanism is crucial for mitigating CO₂ emission and climate changes. Here, we assessed patterns of litter and soil C decomposition after 11 yrs. in-situ N and P addition in a tropical forest where corn leaves or corn roots were added as litter C. The total CO₂ efflux was quantified and partitioned using ¹³C isotope signatures to determine the sources (litter or soil C) every three months. In addition, Changes in C-degrading enzyme activities: β-1,4-glucosidase (BG), phenol oxidase (PHO) and peroxidase (PER), and microbial biomarkers were assessed to interpret the underlying mechanism. Total C-release was enhanced up to17% by the long-term N addition but inhibited up to 15% by P addition. Precisely, N addition only accelerated the litter decomposition and increased about 42% and 6% of the litter C release at 0-5 cm and 5-10 cm soil depths, respectively; while P addition only impeded the soil C decomposition and decreased about 9% and 11% of the soil C release at 0-5 cm and 5-10 cm, respectively. The enhanced C release under N addition might be attributed to the enhanced microbial biomass, the ratio of fungi to bacteria and C-degrading enzyme activities. However, P addition resulted in the reverse result in microbial properties and C-degrading enzyme activities, associated with a decreased C release. Our study suggests that the long-term N and P addition selectively affected the litter and soil C decomposition because of their different physiochemical properties and this tendency might be more pronounced in tropical forests exposed to increasing atmospheric N deposition in the future. The study indicates that the different patterns of litter and soil C decomposition under climate change should be taken account in the future C management strategies.

Understanding Responses of Soil Microbiome to the Nitrogen and Phosphorus Addition in Metasequoia glyptostroboides Plantations of Different Ages

Nitrogen (N) and phosphorus (P) have significant effects on soil microbial community diversity, composition, and function. Also, trees of different life stages have different fertilization requirements. In this study, we designed three N additions and three P levels (5 years of experimental treatment) at two Metasequoia glyptostroboides plantations of different ages (young, 6 years old; middle mature, 24 years old) to understand how different addition levels of N and P affect the soil microbiome. Here, the N fertilization of M. glyptostroboides plantation land (5 years of experimental treatment) significantly enriched microbes (e.g., Lysobacter, Luteimonas, and Rhodanobacter) involved in nitrification, denitrification, and P-starvation response regulation, which might further lead to the decreasing in alpha diversity (especially in 6YMP soil). The P addition could impact the genes involved in inorganic P-solubilization and organic P-mineralization by increasing soil AP and TP. Moreover, the functional differences in the soil microbiomes were identified between the 6YMP and 24YMP soil. This study provides valuable information that improves our understanding on the effects of N and P input on the belowground soil microbial community and functional characteristics in plantations of different stand ages.

A quantitative analysis of microbial community structure-function relationships in plant litter decay

Soil microbes play a central role in ecosystem element cycling. Yet a central question in microbial ecology remains unanswered: to what extent does the taxonomic composition of soil microbial communities mediate biogeochemical process rates? In this quantitative review, we explore the mechanisms that lead to variation in the strength of microbial community structure-function relationships over space and time. To evaluate these mechanisms, we conduct a meta-analysis of studies that have monitored the decomposition of sterilized plant litter inoculated with different microbial assemblages. We find that the influence of microbial community composition on litter decay is pervasive and strong, rivalling in magnitude the influence of litter chemistry on decomposition. However, no single environmental or experimental attribute was correlated with variation in the inoculum effect. These results emphasize the need to better understand ecological dynamics within microbial communities, particularly emergent features such as cross-feeding networks, to improve predictions of soil biogeochemical function.

Harnessing belowground processes for sustainable intensification of agricultural systems

Increasing food demand coupled with climate change pose a great challenge to agricultural systems. In this review we summarize recent advances in our knowledge of how plants, together with their associated microbiota, shape rhizosphere processes. We address (molecular) mechanisms operating at the plant-microbe-soil interface and aim to link this knowledge with actual and potential avenues for intensifying agricultural systems, while at the same time reducing irrigation water, fertilizer inputs and pesticide use. Combining in-depth knowledge about above and belowground plant traits will not only significantly advance our mechanistic understanding of involved processes but also allow for more informed decisions regarding agricultural practices and plant breeding. Including belowground plant-soil-microbe interactions in our breeding efforts will help to select crops resilient to abiotic and biotic environmental stresses and ultimately enable us to produce sufficient food in a more sustainable agriculture in the upcoming decades.

Genome-resolved metagenomics identifies the particular genetic traits of phosphate-solubilizing bacteria in agricultural soil

Bacteria play a key role in phosphate solubilization, but related genome-centric research on agricultural microbiomes is scarce. Here, we reconstructed 472 metagenome-assembled genomes (MAGs) covering agricultural soils from six long-term field trials across China. A total of 79 MAGs contained gcd encoding quinoprotein glucose dehydrogenase (GCD), which is the key biomarker for phosphate solubilization. Our findings showed that all GCD-MAGs represent potentially novel species, with gcd copy numbers varying from 1 to 10 per genome. Large genome size, a high ratio of glycosyl hydrolase genes, and increased capacity for carbohydrate utilization were specific traits of GCD-MAGs. Notably, the gcd copy number showed a significant and positive correlation with genome size. Generated using a machine learning approach, our findings were validated in a dataset of 692 genotypes covering the 18 bacterial families to which the 79 GCD-MAGs belong. Our results improve the knowledge of both the diversity and the genetic composition of phosphate-solubilizing bacteria. In particular, they reveal a genomic link between phosphate solubilization capacity and increased potential for carbohydrate metabolism, which may accelerate targeted engineering and improve management practices for sustainable agriculture.

Strategies of organic phosphorus recycling by soil bacteria: acquisition, metabolism, and regulation

Critical to meeting cellular phosphorus (P) demand, soil bacteria deploy a number of strategies to overcome limitation in inorganic P (P_i ) in soils. As a significant contributor to P recycling, soil bacteria secrete extracellular enzymes to degrade organic P (P_o ) in soils into the readily bioavailable P_i . In addition, several P_o compounds can be transported directly via specific transporters and subsequently enter intracellular metabolic pathways. In this review, we highlight the strategies that soil bacteria employ to recycle P_o from the soil environment. We discuss the diversity of extracellular phosphatases in soils, the selectivity of these enzymes towards various P_o biomolecules and the influence of the soil environmental conditions on the enzyme's activities. Moreover, we outline the intracellular metabolic pathways for P_o biosynthesis and transporter-assisted P_o and P_i uptake at different P_i availabilities. We further highlight the regulatory mechanisms that govern the production of phosphatases, the expression of P_o transporters and the key metabolic changes in P metabolism in response to environmental P_i availability. Due to the depletion of natural resources for P_i , we propose future studies needed to leverage bacteria-mediated P recycling from the large pools of P_o in soils or organic wastes to benefit agricultural productivity.

Genome-Resolved Metagenomics Reveals Distinct Phosphorus Acquisition Strategies between Soil Microbiomes

Enhancing soil phosphate solubilization is a promising strategy for agricultural sustainability, while little is known about the mechanisms of how microorganisms cope with differing phosphorus availability. Using a combination of genome-resolved metagenomics and amplicon sequencing, we investigated the microbial mechanisms involved in phosphorus cycling under three agricultural treatments in a wheat-maize rotation system and two natural reforestation treatments. Available soil phosphorus was the key factor shaping bacterial and fungal community composition and function across our agricultural and reforestation sites. Membrane-bound quinoprotein glucose dehydrogenase (PQQGDH) and exopolyphosphatases (PPX) governed microbial phosphate solubilization in agroecosystems. In contrast, genes encoding glycerol-3-phosphate transporters (ugpB, ugpC, and ugpQ) displayed a significantly greater abundance in the reforestation soils. The gcd gene encoding PQQGDH was found to be the best determinant for bioavailable soil phosphorus. Metagenome-assembled genomes (MAGs) affiliated with Cyclobacteriaceae and Vicinamibacterales were obtained from agricultural soils. Their MAGs harbored not only gcd but also the pit gene encoding low-affinity phosphate transporters. MAGs obtained from reforestation soils were affiliated with Microtrichales and Burkholderiales. These contain ugp genes but no gcd, and thereby are indicative of a phosphate transporter strategy. Our study demonstrates that knowledge of distinct microbial phosphorus acquisition strategies between agricultural and reforestation soils could help in linking microbial processes with phosphorus cycling.

IMPORTANCE The soil microbiome is the key player regulating phosphorus cycling processes. Identifying phosphate-solubilizing bacteria and utilizing them for release of recalcitrant phosphate that is bound to rocks or minerals have implications for improving crop nutrient acquisition and crop productivity. In this study, we combined functional metagenomics and amplicon sequencing to analyze microbial phosphorus cycling processes in natural reforestation and agricultural soils. We found that the phosphorus acquisition strategies significantly differed between these two ecosystems. A microbial phosphorus solubilization strategy dominated in the agricultural soils, while a microbial phosphate transporter strategy was observed in the reforestation soils. We further identified microbial taxa that contributed to enhanced phosphate solubilization in the agroecosystem. These microbes are predicted to be beneficial for the increase in phosphate bioavailability through agricultural practices.

Contrasting effects of carbon source recalcitrance on soil phosphorus availability and communities of phosphorus solubilizing microorganisms

Carbon (C) additions to soil interact through chemical and microbiological processes to cause changes in soil phosphorus (P) availability. However, the response of soil P transformations and relevant microbial communities to C additions having different degrees of recalcitrance remains uncertain. We studied the effects of glucose, hemicellulose and lignin addition on soil P availability, P transformation processes and relevant microbial activity and communities in a P-deficient flooded soil. Lignin significantly increased soil available P concentrations, which was attributed to chemical release of inorganic P and increased alkaline phosphatase activity. Glucose and hemicellulose additions stimulated microbial metabolism of C thereby enhancing microbial demand for P, with increased soil P availability especially in the early incubation period. Glucose or hemicellulose addition changed soil microbial diversity and community composition, leading to enhanced growth and interactions of P solubilizing microorganisms such as Desulfitobacterium, Bacillus and Desulfosporosinus. Our results infer the importance of pH alteration and competitive sorption between PO₄ and functional groups of recalcitrant C (e.g., lignin) with Fe/Al (hydr) oxides in regulating soil P availability. Further, the microbial response to labile C additions led to increased P availability in the P-deficient soil. This study provides important mechanistic information to guide microbially-regulated soil P management in agricultural ecosystems.

Increasing the power of interpretation for soil metaproteomics data

BACKGROUND

Soil and sediment microorganisms are highly phylogenetically diverse but are currently largely under-represented in public molecular databases. Their functional characterization by means of metaproteomics is usually performed using metagenomic sequences acquired for the same sample. However, such hugely diverse metagenomic datasets are difficult to assemble; in parallel, theoretical proteomes from isolates available in generic databases are of high quality. Both these factors advocate for the use of theoretical proteomes in metaproteomics interpretation pipelines. Here, we examined a number of database construction strategies with a view to increasing the outputs of metaproteomics studies performed on soil samples.

RESULTS

The number of peptide-spectrum matches was found to be of comparable magnitude when using public or sample-specific metagenomics-derived databases. However, numbers were significantly increased when a combination of both types of information was used in a two-step cascaded search. Our data also indicate that the functional annotation of the metaproteomics dataset can be maximized by using a combination of both types of databases.

CONCLUSIONS

A two-step strategy combining sample-specific metagenome database and public databases such as the non-redundant NCBI database and a massive soil gene catalog allows maximizing the metaproteomic interpretation both in terms of ratio of assigned spectra and retrieval of function-derived information. Video abstract.

Soil Metaproteomics as a Tool for Environmental Monitoring of Minelands

Opencast mining drastically alters the landscape due to complete vegetation suppression and removal of topsoil layers. Precise indicators able to address incremental changes in soil quality are necessary to monitor and evaluate mineland rehabilitation projects. For this purpose, metaproteomics may be a useful tool due to its capacity to shed light on both taxonomic and functional overviews of soil biodiversity, allowing the linkage between proteins found in soil and ecosystem functioning. We investigated bacterial proteins and peptide abundance of three different mineland rehabilitation stages and compared it with a non-rehabilitated site and a native area (evergreen dense forest) in the eastern Amazon. The total amount of identified soil proteins was significantly higher in the rehabilitating and native soils than in the non-rehabilitated site. Regarding soil bacterial composition, the intermediate and advanced sites were shown to be most similar to native soil. Cyanobacteria and Firmicutes phyla are abundant in the early stages of environmental rehabilitation, while Proteobacteria population dominates the later stages. Enzyme abundances and function in the three rehabilitation stages were more similar to those found in the native soil, and the higher accumulation of many hydrolases and oxidoreductases reflects the improvement of soil biological activity in the rehabilitating sites when compared to the non-rehabilitated areas. Moreover, critical ecological processes, such as carbon and nitrogen cycling, seem to return to the soil in short periods after the start of rehabilitation activities (i.e., 4 years). Metaproteomics revealed that the biochemical processes that occur belowground can be followed throughout rehabilitation stages, and the enzymes shown here can be used as targets for environmental monitoring of mineland rehabilitation projects.

Periphytic microbial response to environmental phosphate bioavailability - relevance to P management in paddy fields

Periphyton occurs widely in shallow-water ecosystems such as paddy fields and plays critical parts in regulating local phosphorus cycling. As such, understanding the mechanisms of the biofilm's response to environmental P variability may lead to better perceptions of P utilization and retention in rice farms. Present study aims at exploring the biological and biochemical processes underlying periphyton's P buffering capability through examining changes in community structure, phosphorus uptake and storage, and molecular makeup of exometabolome at different levels of P availability. Under stressed (both excessive and scarce) phosphorus conditions, we found increased populations of the bacterial genus capable of transforming orthophosphate to polyphosphate, as well as mixotrophic algae who can survive through phagotrophy. These results were corroborated by observed polyphosphate buildup under low and high P treatment. Exometabolomic analyses further revealed that periphytic organisms may substitute S-containing lipids for phospholipids, use siderophores to dissolve iron (hydr)oxides to scavenge adsorbed P, and synthesize auxins to resist phosphorus starvation. These findings not only shed light on the mechanistic insights responsible for driving the periphytic P buffer but attest to the ecological roles of periphyton in aiding plants such as rice to overcome P limitations in natural environment. Importance The ability of periphyton to buffer environmental P in shallow aquatic ecosystems may be a natural lesson on P utilization and retention in paddy fields. This work revealed the routes and tools through which periphytic organisms adapt to and regulate ambient P fluctuation. The mechanistic understanding further implicates that the biofilm may serve rice plants to alleviate P stress. Additional results from extracellular metabolite analyses suggest the dissolved periphytic exometabolome can be a valuable nutrient source for soil microbes and plants to reduce biosynthetic costs. These discoveries have the potential to improve our understanding of biogeochemical cycling of phosphorus in general and to refine P management strategies for rice farm in particular.

Soil Organic Matter Characterization by Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FTICR MS): A Critical Review of Sample Preparation, Analysis, and Data Interpretation

The biogeochemical cycling of soil organic matter (SOM) plays a central role in regulating soil health, water quality, carbon storage, and greenhouse gas emissions. Thus, many studies have been conducted to reveal how anthropogenic and climate variables affect carbon sequestration and nutrient cycling. Among the analytical techniques used to better understand the speciation and transformation of SOM, Fourier transform ion cyclotron resonance mass spectrometry (FTICR MS) is the only technique that has sufficient mass resolving power to separate and accurately assign elemental compositions to individual SOM molecules. The global increase in the application of FTICR MS to address SOM complexity has highlighted the many challenges and opportunities associated with SOM sample preparation, FTICR MS analysis, and mass spectral interpretation. Here, we provide a critical review of recent strategies for SOM characterization by FTICR MS with emphasis on SOM sample collection, preparation, analysis, and data interpretation. Data processing and visualization methods are presented with suggested workflows that detail the considerations needed for the application of molecular information derived from FTICR MS. Finally, we highlight current research gaps, biases, and future directions needed to improve our understanding of organic matter chemistry and cycling within terrestrial ecosystems.

Deep learning for peptide identification from metaproteomics datasets

Metaproteomics is becoming widely used in microbiome research for gaining insights into the functional state of the microbial community. Current metaproteomics studies are generally based on high-throughput tandem mass spectrometry (MS/MS) coupled with liquid chromatography. In this paper, we proposed a deep-learning-based algorithm, named DeepFilter, for improving peptide identifications from a collection of tandem mass spectra. The key advantage of the DeepFilter is that it does not need ad hoc training or fine-tuning as in existing filtering tools. DeepFilter is freely available under the GNU GPL license at https://github.com/Biocomputing-Research-Group/DeepFilter. SIGNIFICANCE: The identification of peptides and proteins from MS data involves the computational procedure of searching MS/MS spectra against a predefined protein sequence database and assigning top-scored peptides to spectra. Existing computational tools are still far from being able to extract all the information out of MS/MS data sets acquired from metaproteome samples. Systematical experiment results demonstrate that the DeepFilter identified up to 12% and 9% more peptide-spectrum-matches and proteins, respectively, compared with existing filtering algorithms, including Percolator, Q-ranker, PeptideProphet, and iProphet, on marine and soil microbial metaproteome samples with false discovery rate at 1%. The taxonomic analysis shows that DeepFilter found up to 7%, 10%, and 14% more species from marine, soil, and human gut samples compared with existing filtering algorithms. Therefore, DeepFilter was believed to generalize properly to new, previously unseen peptide-spectrum-matches and can be readily applied in peptide identification from metaproteomics data.

Characterization of Bacterial and Fungal Communities Reveals Novel Consortia in Tropical Oligotrophic Peatlands

Despite their importance for global biogeochemical cycles and carbon sequestration, the microbiome of tropical peatlands remains under-determined. Microbial interactions within peatlands can regulate greenhouse gas production, organic matter turnover, and nutrient cycling. Here we analyze bacterial and fungal communities along a steep P gradient in a tropical peat dome and investigate community level traits and network analyses to better understand the composition and potential interactions of microorganisms in these understudied systems and their relationship to peatland biogeochemistry. We found that both bacterial and fungal community compositions were significantly different along the P gradient, and that the low-P bog plain was characterized by distinct fungal and bacterial families. At low P, the dominant fungal families were cosmopolitan parasites and endophytes, including Clavicipitaceae (19%) in shallow soils (0-4 cm), Hypocreaceae (50%) in intermediate-depth soils (4-8 cm), and Chaetothyriaceae (45%) in deep soils (24-30 cm). In contrast, high- and intermediate-P sites were dominated by saprotrophic families at all depths. Bacterial communities were consistently dominated by the acidophilic Koribacteraceae family, with the exception of the low-P bog site, which was dominated by Acetobacteraceae (19%) and Syntrophaceae (11%). These two families, as well as Rhodospirillaceae, Syntrophobacteraceae, Syntrophorhabdaceae, Spirochaetaceae, and Methylococcaceae appeared within low-P bacterial networks, suggesting the presence of a syntrophic-methanogenic consortium in these soils. Further investigation into the active microbial communities at these sites, when paired with CH₄ and CO₂ gas exchange, and the quantification of metabolic intermediates will validate these potential interactions and provide insight into microbially driven biogeochemical cycling within these globally important tropical peatlands.

More efficient phosphorus use can avoid cropland expansion

Global projections indicate that approximately 500 Mha of new arable land will be required to meet crop demand by 2050. Applying a dynamic phosphorus (P) pool simulator under different socioeconomic scenarios, we find that cropland expansion can be avoided with less than 7% additional cumulative P fertilizer over 2006-2050 when comparing with cropland expansion scenarios, mostly targeted at nutrient-depleted soils of sub-Saharan Africa. Additional P fertilizer would replenish P withdrawn from crop production, thereby allowing higher productivity levels. We also show that further agronomic improvements such as those that allow for better (legacy) P use in soils could reduce both P outflows to freshwater and coastal ecosystems and the overall demand for P fertilizer.

Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

BACKGROUND

Total DNA (intracellular, iDNA and extracellular, eDNA) from ancient permafrost records the mixed genetic repository of the past and present microbial populations through geological time. Given the exceptional preservation of eDNA under perennial frozen conditions, typical metagenomic sequencing of total DNA precludes the discrimination between fossil and living microorganisms in ancient cryogenic environments. DNA repair protocols were combined with high throughput sequencing (HTS) of separate iDNA and eDNA fraction to reconstruct metagenome-assembled genomes (MAGs) from ancient microbial DNA entrapped in Siberian coastal permafrost.

RESULTS

Despite the severe DNA damage in ancient permafrost, the coupling of DNA repair and HTS resulted in a total of 52 MAGs from sediments across a chronosequence (26-120 kyr). These MAGs were compared with those derived from the same samples but without utilizing DNA repair protocols. The MAGs from the youngest stratum showed minimal DNA damage and thus likely originated from viable, active microbial species. Many MAGs from the older and deeper sediment appear related to past aerobic microbial populations that had died upon freezing. MAGs from anaerobic lineages, including Asgard archaea, however exhibited minimal DNA damage and likely represent extant living microorganisms that have become adapted to the cryogenic and anoxic environments. The integration of aspartic acid racemization modeling and metaproteomics further constrained the metabolic status of the living microbial populations. Collectively, combining DNA repair protocols with HTS unveiled the adaptive strategies of microbes to long-term survivability in ancient permafrost.

CONCLUSIONS

Our results indicated that coupling of DNA repair protocols with simultaneous sequencing of iDNA and eDNA fractions enabled the assembly of MAGs from past and living microorganisms in ancient permafrost. The genomic reconstruction from the past and extant microbial populations expanded our understanding about the microbial successions and biogeochemical alterations from the past paleoenvironment to the present-day frozen state. Furthermore, we provided genomic insights into long-term survival mechanisms of microorganisms under cryogenic conditions through geological time. The combined strategies in this study can be extrapolated to examine other ancient non-permafrost environments and constrain the search for past and extant extraterrestrial life in permafrost and ice deposits on Mars. Video abstract.

Soil microbial communities influencing organic phosphorus mineralization in a coastal dune chronosequence in New Zealand

The Haast chronosequence in New Zealand is an ∼6500-year dune formation series, characterized by rapid podzol development, phosphorus (P) depletion and a decline in aboveground biomass. We examined bacterial and fungal community composition within mineral soil fractions using amplicon-based high-throughput sequencing (Illumina MiSeq). We targeted bacterial non-specific acid (class A, phoN/phoC) and alkaline (phoD) phosphomonoesterase genes and quantified specific genes and transcripts using real-time PCR. Soil bacterial diversity was greatest after 4000 years of ecosystem development and associated with an increased richness of phylotypes and a significant decline in previously dominant taxa (Firmicutes and Proteobacteria). Soil fungal communities transitioned from predominantly Basidiomycota to Ascomycota along the chronosequence and were most diverse in 290- to 392-year-old soils, coinciding with maximum tree basal area and organic P accumulation. The Bacteria:Fungi ratio decreased amid a competitive and interconnected soil community as determined by network analysis. Overall, soil microbial communities were associated with soil changes and declining P throughout pedogenesis and ecosystem succession. We identified an increased dependence on organic P mineralization, as found by the profiled acid phosphatase genes, soil acid phosphatase activity and function inference from predicted metagenomes (PICRUSt2).

Hierarchical Reactivity of Enzyme-Mediated Phosphorus Recycling from Organic Mixtures by Aspergillus niger Phytase

Biological recycling of inorganic phosphorus (P_i) from organic phosphorus (P_o) compounds by phosphatase-type enzymes, including phytases, is an important contributor to the pool of bioavailable P to plants and microorganisms. However, studies of mixed-substrate reactions with these enzymes are lacking. Here, we explore the reactivity of a phytase extract from the fungus Aspergillus niger toward a heterogeneous mixture containing, in addition to phytate, different structures of environmentally relevant P_o compounds such as ribonucleotides and sugar phosphates. Using a high-resolution liquid chromatography-mass spectrometry method to monitor simultaneously the parent P_o compounds and their by-products, we captured sequential substrate-specific evolution of P_i from the mixture, with faster hydrolysis of multiphosphorylated compounds (phytate, diphosphorylated sugars, and di- and tri-phosphorylated ribonucleotides) than hydrolysis of monophosphorylated compounds (monophosphorylated sugars and monophosphorylated ribonucleotides). The interaction mechanisms and energies revealed by molecular docking simulations of each P_o compound within the enzyme's active site explained the substrate hierarchy observed experimentally. Specifically, the favorable orientation for binding of the negatively charged phosphate moieties with respect to the positive potential surface of the active site was important. Collectively, our findings provide mechanistic insights about the broad but hierarchical role of phytase-type enzymes in P_i recycling from the heterogeneous assembly of P_o compounds in agricultural soils or wastes.

Improved sensitivity, accuracy and prediction provided by a high-performance liquid chromatography screen for the isolation of phytase-harbouring organisms from environmental samples

HPLC methods are shown to be of predictive value for classification of phytase activity of aggregate microbial communities and pure cultures. Applied in initial screens, they obviate the problems of ‘false‐positive’ detection arising from impurity of substrate and imprecision of methodologies that rely on phytate‐specific media. In doing so, they simplify selection of candidates for biotechnological applications. Combined with 16S sequencing and simple bioinformatics, they reveal diversity of the histidine phosphatase class of phytases most commonly exploited for biotechnological use. They reveal contribution of multiple inositol‐polyphosphate phosphatase (MINPP) activity to aggregate soil phytase activity, and they identity Acinetobacter spp. as harbouring this prevalent soil phytase activity. Previously, among bacteria MINPP was described exclusively as an activity of gut commensals. HPLC methods have also identified, in a facile manner, a known commercially successful histidine (acid) phosphatase enzyme. The methods described afford opportunity for isolation of phytases for biotechnological use from other environments. They reveal the position of attack on phytate by diverse histidine phosphatases, something that other methods lack.

Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights

Soil is a complex matrix where biotic and abiotic components establish a still unclear network involving bacteria, fungi, archaea, protists, protozoa, and roots that are in constant communication with each other. Understanding these interactions has recently focused on metagenomics, metatranscriptomics and less on metaproteomics studies. Metaproteomic allows total extraction of intracellular and extracellular proteins from soil samples, providing a complete picture of the physiological and functional state of the “soil community”. The advancement of high-performance mass spectrometry technologies was more rapid than the development of ad hoc extraction techniques for soil proteins. The protein extraction from environmental samples is biased due to interfering substances and the lower amount of proteins in comparison to cell cultures. Soil sample preparation and extraction methodology are crucial steps to obtain high-quality resolution and yields of proteins. This review focuses on the several soil protein extraction protocols to date to highlight the methodological challenges and critical issues for the application of proteomics to soil samples. This review concludes that improvements in soil protein extraction, together with the employment of ad hoc metagenome database, may enhance the identification of proteins with low abundance or from non-dominant populations and increase our capacity to predict functional changes in soil.

The Role of Phosphorus Limitation in Shaping Soil Bacterial Communities and Their Metabolic Capabilities

Phosphorus (P) is an essential nutrient that is often in limited supply, with P availability constraining biomass production in many terrestrial ecosystems. Despite decades of work on plant responses to P deficiency and the importance of soil microbes to terrestrial ecosystem processes, how soil microbes respond to, and cope with, P deficiencies remains poorly understood. We studied 583 soils from two independent sample sets that each span broad natural gradients in extractable soil P and collectively represent diverse biomes, including tropical forests, temperate grasslands, and arid shrublands.

Phosphorus (P) is an essential nutrient that is often in limited supply, with P availability constraining biomass production in many terrestrial ecosystems. Despite decades of work on plant responses to P deficiency and the importance of soil microbes to terrestrial ecosystem processes, how soil microbes respond to, and cope with, P deficiencies remains poorly understood. We studied 583 soils from two independent sample sets that each span broad natural gradients in extractable soil P and collectively represent diverse biomes, including tropical forests, temperate grasslands, and arid shrublands. We paired marker gene and shotgun metagenomic analyses to determine how soil bacterial and archaeal communities respond to differences in soil P availability and to detect corresponding shifts in functional attributes. We identified microbial taxa that are consistently responsive to extractable soil P, with those taxa found in low P soils being more likely to have traits typical of oligotrophic life history strategies. Using environmental niche modeling of genes and gene pathways, we found an enriched abundance of key genes in low P soils linked to the carbon-phosphorus (C-P) lyase and phosphonotase degradation pathways, along with key components of the high-affinity phosphate-specific transporter (Pst) and phosphate regulon (Pho) systems. Taken together, these analyses suggest that catabolism of phosphonates is an important strategy used by bacteria to scavenge phosphate in P-limited soils. Surprisingly, these same pathways are important for bacterial growth in P-limited marine waters, highlighting the shared metabolic strategies used by both terrestrial and marine microbes to cope with P limitation.

Phylogenetic conservation of soil bacterial responses to simulated global changes

Soil bacterial communities are altered by anthropogenic drivers such as climate change-related warming and fertilization. However, we lack a predictive understanding of how bacterial communities respond to such global changes. Here, we tested whether phylogenetic information might be more predictive of the response of bacterial taxa to some forms of global change than others. We analysed the composition of soil bacterial communities from perturbation experiments that simulated warming, drought, elevated CO2 concentration and phosphorus (P) addition. Bacterial responses were phylogenetically conserved to all perturbations. The phylogenetic depth of these responses varied minimally among the types of perturbations and was similar when merging data across locations, implying that the context of particular locations did not affect the phylogenetic pattern of response. We further identified taxonomic groups that responded consistently to each type of perturbation. These patterns revealed that, at the level of family and above, most groups responded consistently to only one or two types of perturbations, suggesting that traits with different patterns of phylogenetic conservation underlie the responses to different perturbations. We conclude that a phylogenetic approach may be useful in predicting how soil bacterial communities respond to a variety of global changes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.

Novel phosphate-solubilizing bacteria enhance soil phosphorus cycling following ecological restoration of land degraded by mining

Little is known about the changes in soil microbial phosphorus (P) cycling potential during terrestrial ecosystem management and restoration, although much research aims to enhance soil P cycling. Here, we used metagenomic sequencing to analyse 18 soil microbial communities at a P-deficient degraded mine site in southern China where ecological restoration was implemented using two soil ameliorants and eight plant species. Our results show that the relative abundances of key genes governing soil microbial P-cycling potential were higher at the restored site than at the unrestored site, indicating enhancement of soil P cycling following restoration. The gcd gene, encoding an enzyme that mediates inorganic P solubilization, was predominant across soil samples and was a major determinant of bioavailable soil P. We reconstructed 39 near-complete bacterial genomes harboring gcd, which represented diverse novel phosphate-solubilizing microbial taxa. Strong correlations were found between the relative abundance of these genomes and bioavailable soil P, suggesting their contributions to the enhancement of soil P cycling. Moreover, 84 mobile genetic elements were detected in the scaffolds containing gcd in the 39 genomes, providing evidence for the role of phage-related horizontal gene transfer in assisting soil microbes to acquire new metabolic potential related to P cycling.

Spatial and temporal turnover of soil microbial communities is not linked to function in a primary tropical forest

The spatial and temporal linkages between turnover of soil microbial communities and their associated functions remain largely unexplored in terrestrial ecosystems. Yet defining these relationships and how they vary across ecosystems and microbial lineages is key to incorporating microbial communities into ecological forecasts and ecosystem models. To define linkages between turnover of soil bacterial and fungal communities and their function we sampled fungal and bacterial composition, abundance, and enzyme activities across a 3-ha area of wet tropical primary forest over 2 yr. We show that fungal and bacterial communities both exhibited temporal turnover, but turnover of both groups was much lower than in temperate ecosystems. Turnover over time was driven by gain and loss of microbial taxa and not changes in abundance of individual species present in multiple samples. Only fungi varied over space with idiosyncratic variation that did not increase linearly with distance among sampling locations. Only phosphorus-acquiring enzyme activities were linked to shifts in septate, decomposer fungal abundance; no enzymes were affected by composition or diversity of fungi or bacteria. Although temporal and spatial variation in composition was appreciable, because turnover of microbial communities did not alter the functional repertoire of decomposing enzymes, functional redundancy among taxa may be high in this ecosystem. Slow temporal turnover of tropical soil microbial communities and large functional redundancy suggests that shifts in abundance of particular functional groups may capture ecosystem function more accurately than composition in these heterogeneous ecosystems.

Genome-Resolved Proteomic Stable Isotope Probing of Soil Microbial Communities Using 13CO2 and 13C-Methanol

Stable isotope probing (SIP) enables tracking the nutrient flows from isotopically labeled substrates to specific microorganisms in microbial communities. In proteomic SIP, labeled proteins synthesized by the microbial consumers of labeled substrates are identified with a shotgun proteomics approach. Here, proteomic SIP was combined with targeted metagenomic binning to reconstruct metagenome-assembled genomes (MAGs) of the microorganisms producing labeled proteins. This approach was used to track carbon flows from ¹³CO₂ to the rhizosphere communities of Zea mays, Triticum aestivum, and Arabidopsis thaliana. Rhizosphere microorganisms that assimilated plant-derived ¹³C were capable of metabolic and signaling interactions with their plant hosts, as shown by their MAGs containing genes for phytohormone modulation, quorum sensing, and transport and metabolism of nutrients typical of those found in root exudates. XoxF-type methanol dehydrogenases were among the most abundant proteins identified in the rhizosphere metaproteomes. ¹³C-methanol proteomic SIP was used to test the hypothesis that XoxF was used to metabolize and assimilate methanol in the rhizosphere. We detected 7 ¹³C-labeled XoxF proteins and identified methylotrophic pathways in the MAGs of 8 ¹³C-labeled microorganisms, which supported the hypothesis. These two studies demonstrated the capability of proteomic SIP for functional characterization of active microorganisms in complex microbial communities.

Options for Improved Phosphorus Cycling and Use in Agriculture at the Field and Regional Scales

Soil phosphorus (P) cycling in agroecosystems is highly complex, with many chemical, physical, and biological processes affecting the availability of P to plants. Traditionally, P fertilizer recommendations have been made using an insurance-based approach, which has resulted in the accumulation of P in many intensively managed agricultural soils worldwide and contributed to the widespread water quality issue of eutrophication. To mitigate further environmental degradation and because future P fertilizer supplies are threatened due to finite phosphate rock resources and associated geopolitical and quality issues, there is an immediate need to increase P use efficiency (PUE) in agroecosystems. Through cultivar selection and improved cropping system design, contemporary research suggests that sufficient crop yields could be maintained at reduced soil test P (STP) concentrations. In addition, more efficient P cycling at the field scale can be achieved through agroecosystem management that increases soil organic matter and organic P mineralization and optimizes arbuscular mycorrhizal fungi (AMF) symbioses. This review paper provides a perspective on how agriculture has the potential to utilize plant and microbial traits to improve PUE at the field scale and accordingly, maintain crop yields at lower STP concentrations. It also links with the need to tighten the P cycle at the regional scale, including a discussion of P recovery and recycling technologies, with a particular focus on the use of struvite as a recycled P fertilizer. Guidance on directions for future research is provided.

The effects of phytoremediation on soil bacterial communities in an abandoned mine site of rare earth elements

Overexploitation of rare earth elements (REEs) has caused serious desertification and environmental pollution. The ecological restoration of mining areas has attracted increasing attention in China. Soil microbiota is important for successful ecological remediation of abandoned mine land. In this study, soil samples were collected from a restored REE mine site, and the bacterial community composition and diversity were assessed by Illumina high-throughput sequencing targeting the V3-V4 region of the 16S rRNA gene. Microbiota significantly developed in the remediated land. A total of 663,781 effective 16S rRNA gene sequences were obtained, which were classified into 28 bacterial phyla and 3 archaeal phyla. The dominant phyla across all samples (>5% of total effective sequences) were Proteobacteria, Acidobacteria and Firmicutes. Bacterial diversity indices (OTU number, Shannon index and Chao1 index) of the restored soils were higher than those of the tailings and even surpassed those in the unmined site. Redundancy analysis indicated that soil nutrients (soil organic carbon, available phosphorus and total nitrogen) were the dominant factors, followed by soil pH, affecting bacterial community structure. In general, these results suggested that soil amendment and phytoremediation effectively improved the soil environment of the abandoned mine site, which also increased our understanding of the correlation between microbial variation and soil properties in restored REE mine soils.

Impact of long-term phosphorus fertilizer inputs on bacterial phoD gene community in a maize field, Northeast China

The bacterial phoD gene encodes alkaline phosphomonoesterase, an enzyme which plays an important role in the release of plant-available inorganic phosphorus (P) from organic P in soil. However, the relationships between phoD gene community, alkaline phosphomonoesterase activity, and P availability in soil are poorly understood. In this study, we investigated how alkaline phosphomonoesterase activity, phoD gene abundance, and community structure are influenced by plant-available P using soils (0-10, 10-20 and 20-40 cm) from a long-term field trial in which a continuous maize (Zea mays L.) crop had received different levels of P fertilizer inputs (30, 60 kg P ha^-1 year^-1) for 28 years. Quantitative PCR and high-throughput sequencing were used to analyze phoD gene abundance and community composition. Alkaline phosphomonoesterase enzyme activity was negatively correlated with soil available P, which was reflected in corresponding data for phoD gene abundance. On the other hand, positive correlations were determined between phoD gene α-diversity and available P, while shifts in phoD gene community structure were related to changes in soil pH and P availability. The relative abundance of Pseudomonas was negatively correlated with P availability and positively correlated with alkaline phosphomonoesterase activity, suggesting that Pseudomonas may play an important role in soil organic P mineralization. The findings of this study demonstrated that changes of soil P availability as a result of long-term P fertilizer inputs significantly affected alkaline phosphomonoesterase activity by regulating phoD gene abundance, diversity, as well as altering the phoD gene community composition.