The role of soil redox conditions in microbial phosphorus cycling in humid tropical forests

Labile carbon-induced soil organic matter turnover in a subtropical forest under different redox conditions

Labile organic carbon (LOC) input strongly affects soil organic matter (SOM) dynamics, including gains and losses. However, it is unclear how redox fluctuations regulate these processes of SOM decomposition and formation induced by LOC input. The objective of this study was to explore the impacts of LOC input on SOM turnover under different redox conditions. Soil samples were collected in a subtropical forest. A single pulse of 13C-labeled glucose (i.e., LOC) was applied to the soil. Soil samples were incubated for 40 days under three redox treatments, including aerobic, anoxic, and 10-day aerobic followed by 10-day anoxic conditions. Results showed that LOC input affected soil priming and 13C-SOM accumulation differently under distinct redox conditions by altering the activities of various microorganisms. 13C-PLFAs (phospholipid fatty acids) were analyzed to determine the role of microbial groups in SOM turnover. Increased activities of fungi and gram-positive bacteria (i.e., the K-strategists) by LOC input could ingest metabolites or residues of the r-strategists (e.g., gram-negative bacteria) to result in positive priming. Fungi could use gram-negative bacteria to stimulate priming intensity via microbial turnover in aerobic conditions first. Reduced activities of K-strategists as a result of the aerobic to anoxic transition decreased priming intensity. The difference in LOC retention in SOM under different redox conditions was mainly attributable to 13C-particulate organic carbon (13C-POC) accumulation. Under aerobic conditions, fungi and gram-positive bacteria used derivatives from gram-negative bacteria to reduce newly formed POC. However, anoxic conditions were not conducive to the uptake of gram-negative bacteria by fungi and gram-positive bacteria, favoring SOM retention. This work indicated that redox-regulated microbial activities can control SOM decomposition and formation induced by LOC input. It is extremely valuable for understanding the contribution of soil affected by redox fluctuations to the carbon cycle.

Phosphate-Solubilizing Bacteria: Advances in Their Physiology, Molecular Mechanisms and Microbial Community Effects

Phosphorus is an essential nutrient for all life on earth and has a major impact on plant growth and crop yield. The forms of phosphorus that can be directly absorbed and utilized by plants are mainly HPO42- and H2PO4-, which are known as usable phosphorus. At present, the total phosphorus content of soils worldwide is 400-1000 mg/kg, of which only 1.00-2.50% is plant-available, which seriously affects the growth of plants and the development of agriculture, resulting in a high level of total phosphorus in soils and a scarcity of available phosphorus. Traditional methods of applying phosphorus fertilizer cannot address phosphorus deficiency problems; they harm the environment and the ore material is a nonrenewable natural resource. Therefore, it is imperative to find alternative environmentally compatible and economically viable strategies to address phosphorus scarcity. Phosphorus-solubilizing bacteria (PSB) can convert insoluble phosphorus in the soil into usable phosphorus that can be directly absorbed by plants, thus improving the uptake and utilization of phosphorus by plants. However, there is no clear and systematic report on the mechanism of action of PSB. Therefore, this paper summarizes the discovery process, species, and distribution of PSB, focusing on the physiological mechanisms outlining the processes of acidolysis, enzymolysis, chelation and complexation reactions of PSB. The related genes regulating PSB acidolysis and enzymatic action as well as genes related to phosphate transport and the molecular direction mechanism of its pathway are examined. The effects of PSB on the structure and abundance of microbial communities in soil are also described, illustrating the mechanism of how PSB interact with microorganisms in soil and indirectly increase the amount of available phosphorus in soil. And three perspectives are considered in further exploring the PSB mechanism in utilizing a synergistic multi-omics approach, exploring PSB-related regulatory genes in different phosphorus levels and investigating the application of PSB as a microbial fungicide. This paper aims to provide theoretical support for improving the utilization of soil insoluble phosphorus and providing optimal management of elemental phosphorus in the future.

Exploring the Biologically Active Metabolites Produced by Bacillus cereus for Plant Growth Promotion, Heat Stress Tolerance, and Resistance to Bacterial Soft Rot in Arabidopsis

Eight gene clusters responsible for synthesizing bioactive metabolites associated with plant growth promotion were identified in the Bacillus cereus strain D1 (BcD1) genome using the de novo whole-genome assembly method. The two largest gene clusters were responsible for synthesizing volatile organic compounds (VOCs) and encoding extracellular serine proteases. The treatment with BcD1 resulted in an increase in leaf chlorophyll content, plant size, and fresh weight in Arabidopsis seedlings. The BcD1-treated seedlings also accumulated higher levels of lignin and secondary metabolites including glucosinolates, triterpenoids, flavonoids, and phenolic compounds. Antioxidant enzyme activity and DPPH radical scavenging activity were also found to be higher in the treated seedlings as compared with the control. Seedlings pretreated with BcD1 exhibited increased tolerance to heat stress and reduced disease incidence of bacterial soft rot. RNA-seq analysis showed that BcD1 treatment activated Arabidopsis genes for diverse metabolite synthesis, including lignin and glucosinolates, and pathogenesis-related proteins such as serine protease inhibitors and defensin/PDF family proteins. The genes responsible for synthesizing indole acetic acid (IAA), abscisic acid (ABA), and jasmonic acid (JA) were expressed at higher levels, along with WRKY transcription factors involved in stress regulation and MYB54 for secondary cell wall synthesis. This study found that BcD1, a rhizobacterium producing VOCs and serine proteases, is capable of triggering the synthesis of diverse secondary metabolites and antioxidant enzymes in plants as a defense strategy against heat stress and pathogen attack.

Differential responses and mechanistic controls of soil phosphorus transformation in Eucalyptus plantations with N fertilization and introduced N2 -fixing tree species

Introducing N₂ -fixing tree species into Eucalyptus plantations could replace nitrogen (N) fertilization to maintain high levels of N consumption and productivity. However, N enrichment may exacerbate phosphorus (P) limitation as Eucalyptus robusta Smith is extensively planted in P-poor tropical and subtropical soils. We conducted a field experiment in a pure plantation of Eucalyptus urophylla × grandis to investigate the impacts of N fertilization and introduced an N₂ -fixing tree of Dalbergia odorifera T. Chen on soil P transformation. Nitrogen fertilization significantly enhanced soil occluded P pool and reduced the other P pools due to acidification-induced pH-sensitive geochemical processes, lowering Eucalyptus leaf P concentration with higher N : P ratio. By contrast, introduced N₂ -fixing tree species did not change soil pH, labile inorganic P pool, and Eucalyptus leaf N : P ratio, even enhanced organic P pools and reduced occluded P pool probably due to altering microbial community composition particularly stimulating arbuscular mycorrhiza fungal abundance. Our results revealed differential responses and mechanistic controls of soil P transformation in Eucalyptus plantations with N fertilization and introduced N₂ -fixing tree species. The dissolution of occluded P pool along with organic P accumulation observed in the mixed plantations may represent a promising future to better manage soil P availability.

Warming drives sustained plant phosphorus demand in a humid tropical forest

Phosphorus (P) is often one of the most limiting nutrients in highly weathered soils of humid tropical forests and may regulate the responses of carbon (C) feedback to climate warming. However, the response of P to warming at the ecosystem level in tropical forests is not well understood because previous studies have not comprehensively assessed changes in multiple P processes associated with warming. Here, we detected changes in the ecosystem P cycle in response to a 7-year continuous warming experiment by translocating model plant-soil ecosystems across a 600-m elevation gradient, equivalent to a temperature change of 2.1°C. We found that warming increased plant P content (55.4%) and decreased foliar N:P. Increased plant P content was supplied by multiple processes, including enhanced plant P resorption (9.7%), soil P mineralization (15.5% decrease in moderately available organic P), and dissolution (6.8% decrease in iron-bound inorganic P), without changing litter P mineralization and leachate P. These findings suggest that warming sustained plant P demand by increasing the biological and geochemical controls of the plant-soil P-cycle, which has important implications for C fixation in P-deficient and highly productive tropical forests in future warmer climates.

Response of microbial communities and their metabolic functions to calcareous succession process

Soil chronosequence is of great important in studying rates and directions of soil evolution, which can provide valuable information for the validation of soil genesis theory. However, the variation of microbial composition and structure in a calcareous soil chronosequence in karst region of southwest China is not clear. To reveal the response of microbial communities and their metabolic functions to calcareous succession process, a chronosequence of four calcareous soils (black calcareous soil, brown calcareous soil, yellow calcareous soil and red calcareous soil) with a depth of 0-20 cm from tropical monsoon rainforests of Guangxi Nonggang National Nature Reserve, southwest China was collected to analyze the soil physichemical and microbial properties. The results showed that the overall soil nutrient contents decreased along calcareous soil chronosequences and all calcareous soils were nitrogen (N) limitation. And, there were significant differences in the structure of microbial communities in calcareous soil chronosequences. To accommodate N-restriction, fungal community shifted from pathotroph to symbiotroph trophic pattern and Ectomycorrhizal fungi (ECM) emerged. ECM competing with free-living decomposers for N will slow soil carbon (C) cycling and increase soil C storage. Penicillium and Gaiella, the keystone genera, were related to phosphorus (P) cycle closely. Taken together, the occurrence of these microorganisms emphasizes the importance for C, N and P cycle in calcareous chronosequence soils and thus contributes to the ongoing worldwide endeavor to characterize their function for investigating the rate and direction of calcareous pedogenic changes.

NanoSIP: NanoSIMS Applications for Microbial Biology

High-resolution imaging with secondary ion mass spectrometry (nanoSIMS) has become a standard method in systems biology and environmental biogeochemistry and is broadly used to decipher ecophysiological traits of environmental microorganisms, metabolic processes in plant and animal tissues, and cross-kingdom symbioses. When combined with stable isotope-labeling-an approach we refer to as nanoSIP-nanoSIMS imaging offers a distinctive means to quantify net assimilation rates and stoichiometry of individual cell-sized particles in both low- and high-complexity environments. While the majority of nanoSIP studies in environmental and microbial biology have focused on nitrogen and carbon metabolism (using ¹⁵N and ¹³C tracers), multiple advances have pushed the capabilities of this approach in the past decade. The development of a high-brightness oxygen ion source has enabled high-resolution metal analyses that are easier to perform, allowing quantification of metal distribution in cells and environmental particles. New preparation methods, tools for automated data extraction from large data sets, and analytical approaches that push the limits of sensitivity and spatial resolution have allowed for more robust characterization of populations ranging from marine archaea to fungi and viruses. NanoSIMS studies continue to be enhanced by correlation with orthogonal imaging and 'omics approaches; when linked to molecular visualization methods, such as in situ hybridization and antibody labeling, these techniques enable in situ function to be linked to microbial identity and gene expression. Here we present an updated description of the primary materials, methods, and calculations used for nanoSIP, with an emphasis on recent advances in nanoSIMS applications, key methodological steps, and potential pitfalls.

Effect of P availability on straw-induced priming effect was mainly regulated by fungi in croplands

Phosphorus (P) accumulation in croplands resulting from ever-increasing input of P fertilizer strongly influences soil microbial growth and activities, which is expected to alter the soil priming effect (PE) induced by plant residue. However, the effect of P availability on the magnitude and direction of PE remains largely unexplored and the underlying microbial mechanisms are still unclear. Therefore, a 40-day incubation experiment was established by adding C₄-maize straw to C₃-soils with or without long-term P fertilizer inputs to investigate PE and accompanied dynamics of microbiota. The results revealed that in both soils, straw application caused positive real PEs via a "microbial co-metabolism" mechanism, accompanied by a microbial succession from the dominance of r- and K-strategists to K-strategists (mainly fungi). In addition, long-term amendment with P increased PE by 83.2% compared with no P fertilization control, which was mainly mediated by K-strategists, especially the fungal families Chaetomiaceae and Myrmecridiaceae. The increased PE was accompanied by enhanced microbial biomass carbon, extracellular enzyme activities, and bacterial gene abundance, confirming the "stoichiometric decomposition" theory. Meanwhile, deviating from the conventional paradigm, higher phosphatase activity and lower enzymatic stoichiometry of carbon (C)-to-P ratios in high-P soil compared with that in low-P soil suggested stronger "P mining" with high-P availability.

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil

BACKGROUND

Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures).

RESULTS

We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H218O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients.

CONCLUSIONS

Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks. Video abstract.

Ecological improvement of antimony and cadmium contaminated soil by earthworm Eisenia fetida: Soil enzyme and microorganism diversity

Vermiremediation on improvement of antimony (Sb) and cadmium (Cd) contaminated soil was less reported. In this study, earthworm Eisenia fetida was exposed into soil spiked with Sb and Cd and their mixture for 30 days, and then we measured multiple soil enzyme activities and bacteria communities via enzymatic reaction and high-throughput sequencing of 16 S rRNA genes. The results showed that Sb and Cd at high treatment levels inhibited the activities of urease, neutral phosphatase and protease significantly, but earthworm could promote the activities of urease and neutral phosphatase by 17.75%-121.91% and 1.46%-118.97%, respectively. However, earthworms inhibited catalase and had no effect on protease. The Geometric Mean Index suggested that earthworms led to a higher soil biochemistry function. According to a taxonomic analysis, bacterial community structure predominantly consisted of phylum Proteobacteria, Actinobacteria, Firmicutes, etc. and class Gammaproteobacteria, Actinobacteria, Alphaproteobacteria, etc.; furthermore, Pielou index and Shannon index (Alpha diversity in the habitat) indicated that bacteria diversity and evenness increased in the presence of earthworms. The heating map revealed that earthworms made genus Sphingomonas, Flavobacterium, etc. and species Sphingomonas jaspsi, Conexibacter, etc. dominate. Overall, earthworm is a suitable remediation species to improve the ecological function of heavy metal polluted soil. However, the specific mechanism and causal relationship of how earthworm to control enzyme activity and bacteria community remained to be explored.

Roles of Phosphate Solubilizing Microorganisms from Managing Soil Phosphorus Deficiency to Mediating Biogeochemical P Cycle

Phosphorus (P) is a vital element in biological molecules, and one of the main limiting elements for biomass production as plant-available P represents only a small fraction of total soil P. Increasing global food demand and modern agricultural consumption of P fertilizers could lead to excessive inputs of inorganic P in intensively managed croplands, consequently rising P losses and ongoing eutrophication of surface waters. Despite phosphate solubilizing microorganisms (PSMs) are widely accepted as eco-friendly P fertilizers for increasing agricultural productivity, a comprehensive and deeper understanding of the role of PSMs in P geochemical processes for managing P deficiency has received inadequate attention. In this review, we summarize the basic P forms and their geochemical and biological cycles in soil systems, how PSMs mediate soil P biogeochemical cycles, and the metabolic and enzymatic mechanisms behind these processes. We also highlight the important roles of PSMs in the biogeochemical P cycle and provide perspectives on several environmental issues to prioritize in future PSM applications.

Iron and iron-bound phosphate accumulate in surface soils of ice-wedge polygons in arctic tundra

Phosphorus (P) is a limiting or co-limiting nutrient to plants and microorganisms in diverse ecosystems that include the arctic tundra. Certain soil minerals can adsorb or co-precipitate with phosphate, and this mineral-bound P provides a potentially large P reservoir in soils. Iron (Fe) oxyhydroxides have a high capacity to adsorb phosphate; however, the ability of Fe oxyhydroxides to adsorb phosphate and limit P bioavailability in organic tundra soils is not known. Here, we examined the depth distribution of soil Fe and P species in the active layer (<30 cm) of low-centered and high-centered ice-wedge polygons at the Barrow Environmental Observatory on the Alaska North Slope. Soil reservoirs of Fe and P in bulk horizons and in narrower depth increments were characterized using sequential chemical extractions and synchrotron-based X-ray absorption spectroscopy (XAS). Organic horizons across all polygon features (e.g., trough, ridge, and center) were enriched in extractable Fe and P relative to mineral horizons. Soil Fe was dominated by organic-bound Fe and short-range ordered Fe oxyhydroxides, while soil P was primarily associated with oxides and organic matter in organic horizons but apatite and/or calcareous minerals in mineral horizons. Iron oxyhydroxides and Fe-bound inorganic P (Pi) were most enriched at the soil surface and decreased gradually with depth, and Fe-bound Pi was >4× greater than water-soluble Pi. These results demonstrate that Fe-bound Pi is a large and ecologically important reservoir of phosphate. We contend that Fe oxyhydroxides and other minerals may regulate Pi solubility under fluctuating redox conditions in organic surface soils on the arctic tundra.