Role Of Microbes Research Articles

Single-cell phenotyping of bacteria combined with deep sequencing for improved contextualization of microbiome analyses.

Great effort was made to characterize the bacterial communities inhabiting the human body as a factor in disease, resulting in the realization that a wide spectrum of diseases is associated with an altered composition of the microbiome. However, the identification of disease-relevant bacteria has been hindered by the high cross-sectional diversity of individual microbiomes, and in most cases, it remains unclear whether the observed alterations are cause or consequence of disease. Hence, innovative analysis approaches are required that enable inquiries of the microbiome beyond mere taxonomic cataloging. This review highlights the utility of microbiota flow cytometry, a single-cell analysis platform to directly interrogate cellular interactions, cell conditions, and crosstalk with the host's immune system within the microbiome to take into consideration the role of microbes as critical interaction partners of the host and the spectrum of microbiome alterations, beyond compositional changes. In conjunction with advanced sequencing approaches it could reveal the genetic potential of target bacteria and advance our understanding of taxonomic diversity and gene usage in the context of the microenvironment. Single-cell bacterial phenotyping has the potential to change our perspective on the human microbiome and empower microbiome research for the development of microbiome-based therapy approaches and personalized medicine.

The foul play of two dietary metabolites trimethylamine (TMA) and trimethylamine N-oxide (TMAO) on human health and the role of microbes in mitigating their effects

The foul play of two dietary metabolites trimethylamine (TMA) and trimethylamine N-oxide (TMAO) on human health and the role of microbes in mitigating their effects

S. aureus drives itch and scratch-induced skin damage through a V8 protease-PAR1 axis

Itch is an unpleasant sensation that evokes a desire to scratch. The skin barrier is constantly exposed to microbes and their products. However, the role of microbes in itch generation is unknown. Here, we show that Staphylococcus aureus, a bacterial pathogen associated with itchy skin diseases, directly activates pruriceptor sensory neurons to drive itch. Epicutaneous S.aureus exposure causes robust itch and scratch-induced damage. By testing multiple isogenic bacterial mutants for virulence factors, we identify the S.aureus serine protease V8 as a critical mediator in evoking spontaneous itch and alloknesis. V8 cleaves proteinase-activated receptor 1 (PAR1) on mouse and human sensory neurons. Targeting PAR1 through genetic deficiency, small interfering RNA (siRNA) knockdown, or pharmacological blockade decreases itch and skin damage caused by V8 and S.aureus exposure. Thus, we identify a mechanism of action for a pruritogenic bacterial factor and demonstrate the potential of inhibiting V8-PAR1 signaling to treat itch.

Microbial degradation of marine plastic debris: A comprehensive review on the environmental effects, disposal, and biodegradation

The uncontrolled utilization of plastics and their disposal method presents a global threat owing to their abundance in the marine ecosystem. An exponential upsurge in the practice of synthetic polymers has been reported in the past decade. The degradation of these synthetic polymers is achieved by employing several physiochemical methods. The limited competence of these methods results in the release of hazardous compounds or by-products in the environment. The microbial species isolated from different sources aid in plastic degradation by utilizing them as a sole carbon and energy source. The involvement of microbes in plastic degradation has a profound scope as a cost-effective and eco-friendly alternative to the preexisting techniques. The current review focuses on the environmental effects of plastics and their mitigation through microbial intervention. This review complies with the microplastics and their disposal methods in the environment. The role of microbes and bacterial consortiums in the degradation of plastics and marine plastic debris is also emphasized. The factors affecting microbial degradation and future perspectives were also deliberated in an aspect of environmental welfare.

Geographical survey of the mycobiome and microbiome of Southern California glassy-winged sharpshooters.

The glassy-winged sharpshooter, Homalodisca vitripennis Germar, is an invasive xylem-feeding leafhopper with a devastating economic impact on California agriculture through transmission of the plant pathogen, Xylella fastidiosa. While studies have focused on X. fastidiosa or known symbionts of H. vitripennis, little work has been done at the scale of the microbiome (the bacterial community) or mycobiome (the fungal community). Here, we characterize the mycobiome and the microbiome of H. vitripennis across Southern California and explore correlations with captivity and host insecticide resistance status. Using high-throughput sequencing of the ribosomal internal transcribed spacer 1 region and the 16S rRNA gene to profile the mycobiome and microbiome, respectively, we found that while the H. vitripennis mycobiome significantly varied across Southern California, the microbiome did not. We also observed a significant difference in both the mycobiome and microbiome between captive and wild H. vitripennis. Finally, we found that the mycobiome, but not the microbiome, was correlated with insecticide resistance status in wild H. vitripennis. This study serves as a foundational look at the H. vitripennis mycobiome and microbiome across Southern California. Future work should explore the putative link between microbes and insecticide resistance status and investigate whether microbial communities should be considered in H. vitripennis management practices. IMPORTANCE The glassy-winged sharpshooter is an invasive leafhopper that feeds on the xylem of plants and transmits the devastating pathogen, Xylella fastidiosa, resulting in significant economic damage to California's agricultural system. While studies have focused on this pathogen or obligate symbionts of the glassy-winged sharpshooter, there is limited knowledge of the bacterial and fungal communities that make up its microbiome and mycobiome. To address this knowledge gap, we explored the composition of the mycobiome and the microbiome of the glassy-winged sharpshooter across Southern California and identified differences associated with geography, captivity, and host insecticide resistance status. Understanding sources of variation in the microbial communities associated with the glassy-winged sharpshooter is an important consideration for developing management strategies to control this invasive insect. This study is a first step toward understanding the role microbes may play in the glassy-winged sharpshooter's resistance to insecticides.

Microbially mediated fossil concretions and their characterization by the latest methodologies: a review.

The study of well-preserved organic matter (OM) within mineral concretions has provided key insights into depositional and environmental conditions in deep time. Concretions of varied compositions, including carbonate, phosphate, and iron-based minerals, have been found to host exceptionally preserved fossils. Organic geochemical characterization of concretion-encapsulated OM promises valuable new information of fossil preservation, paleoenvironments, and even direct taxonomic information to further illuminate the evolutionary dynamics of our planet and its biota. Full exploitation of this largely untapped geochemical archive, however, requires a sophisticated understanding of the prevalence, formation controls and OM sequestration properties of mineral concretions. Past research has led to the proposal of different models of concretion formation and OM preservation. Nevertheless, the formation mechanisms and controls on OM preservation in concretions remain poorly understood. Here we provide a detailed review of the main types of concretions and formation pathways with a focus on the role of microbes and their metabolic activities. In addition, we provide a comprehensive account of organic geochemical, and complimentary inorganic geochemical, morphological, microbial and paleontological, analytical methods, including recent advancements, relevant to the characterization of concretions and sequestered OM. The application and outcome of several early organic geochemical studies of concretion-impregnated OM are included to demonstrate how this underexploited geo-biological record can provide new insights into the Earth's evolutionary record. This paper also attempts to shed light on the current status of this research and major challenges that lie ahead in the further application of geo-paleo-microbial and organic geochemical research of concretions and their host fossils. Recent efforts to bridge the knowledge and communication gaps in this multidisciplinary research area are also discussed, with particular emphasis on research with significance for interpreting the molecular record in extraordinarily preserved fossils.

Narrow host range phages infect essential bacteria for water purification reactions in groundwater-fed rapid sand filters

Biofiltration is used worldwide to provide safe potable water due to its low energy demand and excellent treatment performance. For instance, in Denmark, over 95% of drinking water is supplied through groundwater-fed rapid sand filters (RSF). Bacteriophages, viruses that infect bacteria, have been shown to shape the taxonomic and functional composition of microbial communities across a range of natural and engineering systems. However, phages in the biofiltration systems are rarely studied, despite the central role microbes play in water purification. To probe this, metagenomic data from surface water, groundwater and mixed source water biofiltration units (n = 26 from China, Europe and USA) for drinking water production were analysed to characterize prokaryotic viruses and to identify their potential microbial hosts. The source water type and geographical location are found to exert influence on the composition of the phageome in biofilters. Although the viral abundance (71,676 ± 17,841 RPKM) in biofilters is only 14.4% and 17.0% lower than those of the nutrient-rich wastewater treatment plants and fresh surface waters, the richness (1,441 ± 1,046) and diversity (Inverse Simpson: 91 ± 61) in biofiltration units are significantly less by a factor of 2–5 and 3–4, respectively. In depth analysis of data from 24 groundwater-fed RSFs in Denmark revealed a core phageome shared by most RSFs, which was consistently linked to dominant microbial hosts involved in key biological reactions for water purification. Finally, the high number of specific links detected between phages and bacterial species and the large proportion of lytic phages (77%) led to the conjecture that phages regulate bacterial populations through predation, preventing the proliferation of dominant species and contributing to the established functional redundancy among the dominant microbial groups. In conclusion, bacteriophages are likely to play a significant role in water treatment within biofilters, particularly through interactions with key bacterial species.

Characteristics of Early Neoproterozoic Stromatolites from Southern Liaoning, North China: Insights into the Formation of Stromatolites

Stromatolites, among the earliest fossils in Earth’s history, are widely distributed on the margins of the North China Precambrian carbonate platform. The formation processes of stromatolites reveal the biomineralization and evolution of early life in the Precambrian. The well-preserved stromatolitic dolostones recorded in the Ganjingzi Formation are developed around Yuanjiagou village, in southern Liaoning Province. The morphology of the Ganjingzi stromatolites manifests in stratiform, columnar, and domal forms. A tripartite lamina structure including light laminae and two types of dark laminae is observed in thin sections. The origins of dark laminae were related to microbial metabolism, while the light laminae were the result of the recrystallization of synsedimentary marine cement. Hardground substrate and carbonate fragments were suitable for microbes to colonize, suggesting that microbes can adapt to various current energy settings. A comparison of the growth environment, morphology, and laminae features between the Ganjingzi stromatolites and modern carbonate stromatolites from Hamelin Pool and Lagoa Vermelha suggest that the Ganjingzi stromatolites may have been formed in a restricted tidal-flat setting with high salinity and evaporation. The role of microbes that form modern stromatolites in inducing precipitation of carbonate or binding sediments, might contribute to the formation of the Ganjingzi stromatolites. The formation process of the Ganjingzi stromatolites indicates that the microbial communities, favorable substrate, and synsedimentary marine cement were the key factors in promoting the development of the Neoproterozoic stromatolites on the northeastern margin of the North China Craton.

Integration of multi-omics data to elucidate keystone unknown taxa within microbialite-forming ecosystems.

Microbes continually shape Earth's biochemical and physical landscapes by inhabiting diverse metabolic niches. Despite the important role microbes play in ecosystem functioning, most microbial species remain unknown highlighting a gap in our understanding of structured complex ecosystems. To elucidate the relevance of these unknown taxa, often referred to as "microbial dark matter," the integration of multiple high throughput sequencing technologies was used to evaluate the co-occurrence and connectivity of all microbes within the community. Since there are no standard methodologies for multi-omics integration of microbiome data, we evaluated the abundance of "microbial dark matter" in microbialite-forming communities using different types meta-omic datasets: amplicon, metagenomic, and metatranscriptomic sequencing previously generated for this ecosystem. Our goal was to compare the community structure and abundances of unknown taxa within the different data types rather than to perform a functional characterization of the data. Metagenomic and metatranscriptomic data were input into SortMeRNA to extract 16S rRNA gene reads. The output, as well as amplicon sequences, were processed through QIIME2 for taxonomy analysis. The R package mdmnets was utilized to build co-occurrence networks. Most hubs presented unknown classifications, even at the phyla level. Comparisons of the highest scoring hubs of each data type using sequence similarity networks allowed the identification of the most relevant hubs within the microbialite-forming communities. This work highlights the importance of unknown taxa in community structure and proposes that ecosystem network construction can be used on several types of data to identify keystone taxa and their potential function within microbial ecosystems.

Role of microbial electrosynthesis system in CO2 capture and conversion: a recent advancement toward cathode development.

Microbial electrosynthesis (MES) is an emerging electrochemical technology currently being researched as a CO2 sequestration method to address climate change. MES can convert CO2 from pollution or waste materials into various carbon compounds with low energy requirements using electrogenic microbes as biocatalysts. However, the critical component in this technology, the cathode, still needs to perform more effectively than other conventional CO2 reduction methods because of poor selectivity, complex metabolism pathways of microbes, and high material cost. These characteristics lead to the weak interactions of microbes and cathode electrocatalytic activities. These approaches range from cathode modification using conventional engineering approaches to new fabrication methods. Aside from cathode development, the operating procedure also plays a critical function and strategy to optimize electrosynthesis production in reducing operating costs, such as hybridization and integration of MES. If this technology could be realized, it would offer a new way to utilize excess CO2 from industries and generate profitable commodities in the future to replace fossil fuel-derived products. In recent years, several potential approaches have been tested and studied to boost the capabilities of CO2-reducing bio-cathodes regarding surface morphology, current density, and biocompatibility, which would be further elaborated. This compilation aims to showcase that the achievements of MES have significantly improved and the future direction this is going with some recommendations. Highlights - MES approach in carbon sequestration using the biotic component.- The role of microbes as biocatalysts in MES and their metabolic pathways are discussed.- Methods and materials used to modify biocathode for enhancing CO2 reduction are presented.

Microbial-driven carbon fixation in natural wetland.

With the development of global industrialization, carbon neutrality has become an issue that we must be paid attention to. Microorganisms not only have an important impact on the carbon chemical cycle between the Earth's biosphere and biogeography but also play a key role in maintaining the global organic carbon balance. Wetlands are the main reservoir of organic carbon in the mainland of China, and wetland carbon sinks are indispensable for China to achieve the goal of "dual carbon," and China has taken the consolidation and improvement of wetland carbon sink capacity as an important part of the carbon peaking action plan. As a unique low-latitude, high-altitude seasonal plateau wetland in China, Napahai shows high research value. However, the role of microbes in maintaining dissolved organic carbon balance in this area has not been reported. In the study, six carbon fixation genes, accA, aclB, acsA, acsB, cbbL, and rbcL, were analyzed based on metagenomics to elucidate the rich genetic diversity, uniqueness and differences in the Napahai plateau wetland. It was found that the microbial diversity in the Napahai plateau wetland was different from other habitats. In addition, the aclB gene, a rare taxon with high genetic diversity and rich species in the Napahai plateau wetland, played a key role in the microbial metabolic pathway. Finally, the construction of a metabolic pathway through the Kyoto encyclopedia for genes and genomes revealed the contribution of microbes to carbon fixation and the role of microbes in maintaining the organic carbon balance of the Napahai plateau wetland.

Microbially Induced Calcium Carbonate Precipitation by Sporosarcina pasteurii: a Case Study in Optimizing Biological CaCO3 Precipitation.

Current production of traditional concrete requires enormous energy investment that accounts for approximately 5 to 8% of the world's annual CO2 production. Biocement is a building material that is already in industrial use and has the potential to rival traditional concrete as a more convenient and more environmentally friendly alternative. Biocement relies on biological structures (enzymes, cells, and/or cellular superstructures) to mineralize and bind particles in aggregate materials (e.g., sand and soil particles). Sporosarcina pasteurii is a workhorse organism for biocementation, but most research to date has focused on S. pasteurii as a building material rather than a biological system. In this review, we synthesize available materials science, microbiology, biochemistry, and cell biology evidence regarding biological CaCO3 precipitation and the role of microbes in microbially induced calcium carbonate precipitation (MICP) with a focus on S. pasteurii. Based on the available information, we provide a model that describes the molecular and cellular processes involved in converting feedstock material (urea and Ca2+) into cement. The model provides a foundational framework that we use to highlight particular targets for researchers as they proceed into optimizing the biology of MICP for biocement production.

Unraveling the roles of coastal bacterial consortia in degradation of various lignocellulosic substrates.

Lignocellulose, as the most abundant natural organic carbon on earth, plays a key role in regulating the global carbon cycle, but there have been only few studies in marine ecosystems. Little information is available about the extant lignin-degrading bacteria in coastal wetlands, limiting our understanding of their ecological roles and traits in lignocellulose degradation. We utilized in situ lignocellulose enrichment experiments coupled with 16S rRNA amplicon and shotgun metagenomics sequencing to identify and characterize bacterial consortia attributed to different lignin/lignocellulosic substrates in the southern-east intertidal zone of East China Sea. We found the consortia enriched on woody lignocellulose showed higher diversity than those on herbaceous substrate. This also revealed substrate-dependent taxonomic groups. A time-dissimilarity pattern with increased alpha diversity over time was observed. Additionally, this study identified a comprehensive set of genes associated with lignin degradation potential, containing 23 gene families involved in lignin depolymerization, and 371 gene families involved in aerobic/anaerobic lignin-derived aromatic compound pathways, challenging the traditional view of lignin recalcitrance within marine ecosystems. In contrast to similar cellulase genes among the lignocellulose substrates, significantly different ligninolytic gene groups were observed between consortia under woody and herbaceous substrates. Importantly, we not only observed synergistic degradation of lignin and hemi-/cellulose, but also pinpointed the potential biological actors at the levels of taxa and functional genes, which indicated that the alternation of aerobic and anaerobic catabolism could facilitate lignocellulose degradation. Our study advances the understanding of coastal bacterial community assembly and metabolic potential for lignocellulose substrates. IMPORTANCE It is essential for the global carbon cycle that microorganisms drive lignocellulose transformation, due to its high abundance. Previous studies were primarily constrained to terrestrial ecosystems, with limited information about the role of microbes in marine ecosystems. Through in situ lignocellulose enrichment experiment coupled with high-throughput sequencing, this study demonstrated different impacts that substrates and exposure times had on long-term bacterial community assembly and pinpointed comprehensive, yet versatile, potential decomposers at the levels of taxa and functional genes in response to different lignocellulose substrates. Moreover, the links between ligninolytic functional traits and taxonomic groups of substrate-specific populations were revealed. It showed that the synergistic effect of lignin and hemi-/cellulose degradation could enhance lignocellulose degradation under alternation of aerobic and anaerobic conditions. This study provides valuable taxonomic and genomic insights into coastal bacterial consortia for lignocellulose degradation.

Bacteria rather than fungi mediate the chemodiversity of dissolved organic matter in a mudflat intertidal zone

Dissolved organic matter (DOM) in natural ecosystems is intimately associated with microbial communities. However, it remains unclear whether the diversity patterns followed by microbes can be transmitted to DOM compounds. Considering the structural properties of DOM compounds and the roles of microbes in ecosystems, we hypothesized that bacteria tended to be more closely associated with DOM compounds than fungi. To test the above hypothesis and bridge this knowledge gap, the diversity patterns and ecological processes for the DOM compounds, and the bacterial and fungal communities in a mudflat intertidal zone were comparatively investigated. As a result, spatial scaling patterns followed by microbes, including the diversity-area and distance-decay relationships, were also observed for DOM compounds. Lipid-like and aliphatic-like molecules comprised the major DOM compounds associated with environmental factors. Both the alpha- and beta-chemodiversity of DOM compounds were significantly associated with the diversity of bacterial communities, but not fungal communities. Co-occurrence ecological network analysis suggested that DOM compounds were more frequently associated with bacteria than fungi. Further, consistent community assembly patterns were observed for DOM and bacterial communities, but not fungal communities. Integrating multiple lines of evidence, this study demonstrated that bacteria rather than fungi mediated the chemodiversity of DOM in the mudflat intertidal zone. This study elucidates the spatial patterns of complex dissolved organic matter (DOM) pools in the intertidal ecosystem, shedding light on the intricate relationship between DOM compounds and bacterial communities.

Biliary microbial patterns in primary sclerosing cholangitis are linked to poorer transplant-free survival.

Factors that determine individual disease course of patients with primary sclerosing cholangitis (PSC) are poorly understood. Although an association between gut microbes and disease outcome has been suggested, little is known about the role of microbes in the biliary tract. We analyzed microbial cultures from bile specimens obtained during routine endoscopic retrograde cholangiopancreatography (ERCP) and intraoperatively before liver transplantation in 114 patients with PSC in our tertiary academic center. The presence of bacterial and fungal species was correlated with clinical characteristics and outcome data. A total of 87 patients (76%) had positive bile culture results. The presence of concomitant inflammatory bowel disease (IBD) was associated with positive bile culture results in multivariate analysis (OR, 4.707; 95% CI, 1.688-13.128; p=0.003). Enterococcus spp. in the bile was associated with a more frequent occurrence of liver transplantation and/or death (OR, 2.778; 95% CI, 1.147-6.728; p=0.021) and recurrent (≥3) cholangitis episodes (OR, 2.839; 95% CI, 1.037-7.768; p=0.037). Biliary candidiasis was linked to a higher frequency of recurrent (≥3) cholangitis episodes (OR, 5.677; 95% CI, 1.940-16.616; p=0.001). Proton pump inhibitor intake conferred a clinical feature associated with biliary candidiasis in multivariate analysis (OR, 3.559; 95% CI, 1.275-9.937; p=0.016). Our data indicate that in patients with PSC, presence of Enterococcus spp. and Candida spp. in bile is associated with an adverse outcome. Concomitant IBD is linked to presence of microbes in bile, and proton pump inhibitor intake is a feature associated with biliary candidiasis in patients with PSC.

Identification of Putative Bacterial Pathogens for Orofacial Granulomatosis Based on 16S rRNA Metagenomic Analysis.

Orofacial granulomatosis (OFG) is a chronic inflammatory disease characterized by nontender swelling of the orofacial tissues, the underlying cause of which remains unknown. Our previous study demonstrated that tooth apical periodontitis (AP) is involved in the development of OFG. To characterize the AP bacterial signatures of OFG patients and identify possible pathogenic bacteria that cause OFG, the compositions of the AP microbiotas in OFG patients and controls were compared using 16S rRNA gene sequencing. Pure cultures of putative bacterial pathogens were established by growing bacteria as colonies followed by purification, identification, and enrichment and then were injected into animal models to determine the causative bacteria contributing to OFG. A specific AP microbiota signature in the OFG patients was shown, characterized by the predominance of phyla Firmicutes and Proteobacteria, notably members of the genera Streptococcus, Lactobacillus, and Neisseria, were found. Streptococcus spp., Lactobacillus casei, Neisseria subflava, Veillonella parvula, and Actinomyces spp. from OFG patients were isolated and successfully cultured in vitro and then injected into mice. Ultimately, footpad injection with N. subflava elicited granulomatous inflammation. IMPORTANCE Infectious agents have long been considered to play a role in the initiation of OFG; however, a direct causal relationship between microbes and OFG has not yet been established. In this study, a unique AP microbiota signature was identified in OFG patients. Moreover, we successfully isolated candidate bacteria from AP lesions of OFG patients and assessed their pathogenicity in laboratory mice. Findings from this study may help provide in-depth insights into the role of microbes in OFG development, providing the basis for targeted therapeutic approaches for OFG.

Habitat heterogeneity effects on microbial communities of the Gulf of Maine

Many biological and physical variables influence microbes at the sediment-water interface, whose response to those variables affects the overall fate and residence time of organic matter (OM) in the marine environment. In addition to the many ecological roles microbes play in deep-sea sediments, further studies are needed to address microbial community diversity and its influence on seafloor organic matter remineralization rates. We explored microbial diversity, distribution, and associated organic matter remineralization among contrasting habitats and following 24-h experimental phytodetrital enrichment of sediments from Canyon, Inter-Canyon, and Channel habitats of the Gulf of Maine, Northwest Atlantic. Based on multivariate analyses of community composition we found that habitat heterogeneity influenced microbial community composition but not microbial diversity. Similarly, the phytodetrital addition did not translate to significant differences in microbial diversity but altered nitrate flux in Inter-canyon sediments and phosphate flux in Channel sediments. Bacteria were dominant over Archaea and, of the environmental variables we measured, quantity and quality of organic matter best explained overall microbial community variation. Proteobacteria, Bacteroidae, Acidobacteriota, Planctomycetota, and NB1-J Deltaproteobacteria dominated all habitats, but variation in the microbial community at our study sites explained only 7% of nutrient fluxes. Our exploratory study did not suggest a strong contribution of microbial community composition to OM remineralization variation both among contrasting habitats and in response to phytodetrital addition, and thus to this aspect of deep-sea ecosystem functioning, at least over short-term incubations.

Divergent accumulation of microbial and plant necromass along paddy soil development in a millennium scale

Plant inputs and their subsequent microbial transformations drive the formation and accumulation of soil organic carbon (SOC). Rice paddy is more conducive to SOC accumulation than uplands, primarily because of predominant anaerobic conditions. However, the role of microbes and plants in the buildup of SOC under prolonged rice cultivation has not been well explored in the literature. In a millennium-scale paddy soil chronosequence, we used amino sugars (AS) and lignin phenols (LN) as tracers to investigate microbial and plant-derived necromass changes and evaluated their contributions to SOC accumulation with increasing rice cultivation duration. Across the 1000-year rice cultivation process, AS and LN contents increased with SOC accumulation. Soil pH and salinity are considered to play vital roles in regulating the retention of AS and LN. In contrast to the control of soil enzyme activity on LN accrual (e.g., peroxidase), the microbial biomass and fungi-to-bacteria ratio greatly affected AS accumulation in paddy soil. The components of AS and LN also changed with time, exhibiting a significant accumulation of galactosamine and cinnamyl phenol units in the late stage. Long-term rice cultivation is more conducive to the accumulation of bacterial residues. AS demonstrated a greater contribution to SOC than LN compounds within 100 years, whereas the contribution of LN ultimately exceeded AS in the late stage. Concurrently, we found a higher degree of oxidative lignin degradation in younger soils and reduced degradation with increasing duration of rice paddy cultivation. The accumulation of microbial necromass is more than plant necromass in the early stage, and it is the opposite in the late stage. Our results are critical to understand the formation and sequestration processes of SOC in paddy soils.

Potential effect of key soil bacterial taxa on the increase of rice yield under milk vetch rotation.

Legume crop rotation is often adopted in rice cultivation to improve soil productivity. However, little is known about the role of microbes under legume rotation in affecting soil productivity. To elucidate this, a long-term paddy cropping experiment was set up to study the relationship between crop yield, soil chemical properties, and key microbial taxa under a double-rice and milk vetch rotation. Milk vetch rotation significantly improved soil chemical properties compared to no fertilization treatment, and soil phosphorus was a major factor correlated with crop yield. Long-term legume rotation increased soil bacterial alpha diversity and changed soil bacterial community. After milk vetch rotation, the relative abundances of Bacteroidota, Desulfobacterota, Firmicutes, and Proteobacteria increased while those of Acidobacteriota, Chloroflexi, and Planctomycetota decreased. Moreover, milk vetch rotation increased the relative abundance of phosphorus-related gene K01083 (bpp), which was significantly correlated with soil phosphorus content and crop yield. Network analysis showed that taxa of Vicinamibacterales were positively correlated with total phosphorus and available phosphorus, which was a potential taxon contributing to the availability of soil phosphorus stock. Our results indicated that milk vetch rotation could enrich key taxa with latent phosphate-solubilizing ability, increase the content of soil available phosphorus, and finally enhance crop yield. This could provide scientific guidance for better crop production.

Special Issue on Role of Microbes in Agriculture and Food

Microorganisms play an important role in human life by influencing agricultural crops, which are raw materials used in the production of food [...]