Nitrogenase gene diversity and microbial community structure: a cross-system comparison

The influence of rhizosphere soil microorganisms and environmental factors on gentiopicroside content in the roots and rhizomes of Gentiana scabra Bunge from Liaoning Province

Background

Rhizosphere soil microorganisms, as the second genome of plants, play an important role in the formation of secondary metabolites of medicinal plants and are one of the key factors in the formation of the authenticity of medicinal materials.

Methods

In this paper, the rhizosphere soils of Gentiana scabra Bunge from six producing areas in Liaoning Province were taken as the research objects. Through high-throughput sequencing technology, and with the help of PLS-DA and RDA, the impacts of rhizosphere soil microorganisms and environmental factors on the quality of G. scabra were explored in depth.

Results

Alpha diversity shows that the diversity of bacterial communities varies significantly, while the regularity of fungi is weak; beta diversity shows that samples from different producing areas can be effectively grouped according to community structure. LDA effect shows that the differential species of bacteria and fungi vary among different producing areas. Indicator and random forest analysis show that Sphingomonas and Subgroup_2 are the main indicator species of the bacterial communities in the high-content group, which can increase the evenness of microbial communities and maintain or enhance species diversity. The regularity of fungal communities is relatively weak. Functional metagenomic analysis shows that the functions of soil microorganisms in the six producing areas are similar but the relative abundances are different. The main functions of bacteria are closely related to microbial metabolism in diverse environments, biosynthesis of secondary metabolites, metabolic pathways, etc.; fungi are mainly lichen parasite, plant saprotroph, and ericoid mycorrhizal. PLS-DA and RDA analysis show that properly adjusting the key environmental factors of Ca, pH, and rapidly available potassium, which have a great influence on G. scabra, can affect the abundances of microorganisms such as Subgroup_2, Burkholderia-Caballeronia-Paraburkholderia, Metarhizium, Bryobacter, Fusarium, Rhodanobacter, Cladophialophora, Sphingomonas and Trichoderma, and then regulate the content of gentiopicroside.

Discussion

This study provides practical microbial approaches and strategies for improving gentiopicroside content in the roots and rhizomes of G. scabra, and lays a solid scientific foundation for ensuring the quality and safety of genuine medicinal materials and the stable and sustainable development of the G. scabra planting industry.

Multiple Plant Growth-Promoting Activities Exhibited by Root-Associated Bacteria Isolated From Bamboo and Corn

Plant growth-promoting bacteria found in the plant roots and rhizosphere stimulate growth and reduce plant diseases through various direct and indirect mechanisms. They are proven as efficient biofertilizers that enable farmers to reduce or eliminate the use of expensive and environmentally harmful chemical fertilizers. The goal of this study was to isolate, characterize, and identify nitrogen-fixing bacteria with additional plant growth-promoting traits from the roots of bamboo (Bambusa sp.) and corn (Zea mays L.) grown in Cagayan Province, Philippines. A total of 27 bacteria were isolated and identified based on 16S rRNA gene sequencing and phylogenetic analysis. Selected isolates were also subjected to whole-genome sequencing to obtain accurate identification. The isolates were classified into 12 genera, the majority of which belonged to Leclercia, Pantoea, Klebsiella, and Exiguobacterium. Assays for four plant growth-promoting activities revealed that all isolates exhibited at least two activities in vitro. Four isolates (15%) tested positive for the nitrogen-fixation gene nifH, which was mostly detected in Klebsiella isolates. Eleven (41%) solubilized phosphate and Pantoea isolates showed the highest potential. All strains (100%) synthesized indole-3-acetic acid (IAA), and 24 (89%) produced siderophores. Notably, Enterobacter roggenkampii strain B1-01 and Klebsiella oxytoca strain B1-04 displayed all the examined plant growth-promoting traits. Our findings demonstrated that the roots of bamboo and corn host a variety of beneficial bacteria exhibiting significant plant growth-promoting activities under in vitro conditions. These strains could be used for future investigations into microbe-plant interactions and have the potential to be harnessed for various agricultural applications.

Mucilage produced by aerial roots hosts diazotrophs that provide nitrogen in Sorghum bicolor

Sorghum (Sorghum bicolor) is an important food, feed, and fodder crop worldwide and is gaining popularity as an energy crop due to its high potential for biomass production. Some sorghum accessions develop many aerial roots and produce an abundant carbohydrate-rich mucilage after rain. This aerial root mucilage is similar to that observed in landraces of maize (Zea mays) from southern Mexico, which have been previously shown to host diazotrophs. In this study, we characterized the aerial root development of several sorghum accessions and the impact of humidity on this trait. We conducted a microbiome study of the aerial root mucilage of maize and sorghum and isolated numerous diazotrophs from field sorghum mucilage. We observed that the prevailing phyla in the mucilage were Pseudomonadota, Bacteroidota, and Bacillota. However, bacterial abundances varied based on the genotype and the location. Using acetylene reduction, 15N2 gas feeding, and 15N isotope dilution assays, we confirmed that these sorghum accessions can acquire about 40% of their nitrogen from the atmosphere through these associations on aerial roots. Nitrogen fixation in sorghum aerial root mucilage offers a promising avenue to reduce reliance on synthetic fertilizers and promote sustainable agricultural practices for food, feed, fodder, and bioenergy production.

Fine-scale diazotroph community structure in the continental slope of the northern South China sea

Diazotrophs have made significant contributions to marine nitrogen cycles. However, their distribution patterns and determined mechanisms have not been fully understood, particularly at the small regional scales. Here, the diazotrophic community structure by different sample sizes (0.2-10 μm and >10 μm), evaluated using high-throughput sequencing of the nifH gene, and the abundance of four typical diazotroph phylotypes, estimated by quantitative PCR of the nifH gene, were investigated on the continental slope of the northern South China Sea at a horizontal spatial resolution of 47.19-71.63 km. The results showed that Proteobacteria and Cyanobacteria were the dominant diazotrophic groups, which mainly contributed by Gamma-proteobacteria and Trichodesmium, respectively. Trichodesmium occupied the large-particle samples in the surface water, while other diazotrophs were nonuniformly distributed across water depths, particle sizes, and stations, indicating the heterogeneous distribution of diazotrophs at fine scales. Vertical profiles of environmental factors, especially the profile data of Fe concentration, were investigated, and the results indicated that temperature, dissolved inorganic nitrogen, and N:Fe were strongly correlated to diazotroph abundance and distribution of Trichodesmium and γ-24774A11. In the transect influenced by the Pearl River plume, γ-24774A11 nifH gene abundance significantly decreased than in other stations, indicating the important role of Pearl River plume in shaping the diazotrophic community structure. These findings advance our understanding of diazotrophic biogeography at the smaller regional scales.

Unelongated Stems are an Active Nitrogen-Fixing Site in Rice Stems Supported by Both Sugar and Methane Under Low Nitrogen Conditions

Enhancing nitrogen (N) fixation in rice plants can reduce N fertilizer application and contribute to sustainable rice production, particularly under low-N conditions. However, detailed microbial and metabolic characterization of N fixation in rice stems, unlike in the well-studied roots, has not been investigated. Therefore, the aim of this study was to determine the active N-fixing sites, their diazotroph communities, and the usability of possible carbon sources in stems compared with roots. The N-fixing activity and copy number of the nitrogenase gene in the rice stem were high in the outer part of the unelongated stem (basal node), especially in the epidermis. N fixation, estimated using the acetylene reduction assay, was also higher in the leaf sheath and root than in the inner part of the unelongated stem and culm. Amplicon sequence variants (ASVs) close to sugar-utilizing heterotrophic diazotrophs belonging to Betaproteobacteria and type II methanotrophic diazotrophs belonging to Alphaproteobacteria were abundant in the outer part of the unelongated stems. Media containing crushed unelongated stems exhibited N-fixing activity when sucrose, glucose, and methane were added as the sole carbon sources. This suggested that N fixation in the unelongated stems was at least partly supported by sugars (sucrose and glucose) and methane as carbon sources. ASVs close to sugar-utilizing heterotrophs belonging to Actinobacteria were also highly abundant in the unelongated stem; however, their functions need to be further elucidated. The present finding that diazotrophs in rice stems can use sugars such as sucrose and glucose synthesized by rice plants provides new insights into enhancing N fixation in rice stems.

Bacterial Isolation from Natural Grassland on Nitrogen-Free Agar Yields Many Strains Without Nitrogenase

Nitrogen inputs for sustainable crop production for a growing population require the enhancement of biological nitrogen fixation. Efforts to increase biological nitrogen fixation include bioprospecting for more effective nitrogen-fixing bacteria. As bacterial nitrogenases are extremely sensitive to oxygen, most primary isolation methods rely on the use of semisolid agar or broth to limit oxygen exposure. Without physical separation, only the most competitive strains are obtained. The distance between strains provided by plating on solid media in reduced oxygen environments has been found to increase the diversity of culturable potential diazotrophic bacteria. To obtain diverse nitrogen-fixing isolates from natural grasslands, we plated soil suspensions from 27 samples onto solid nitrogen-free agar and incubated them under atmospheric and oxygen-reducing conditions. Putative nitrogen fixers were confirmed by subculturing in liquid nitrogen-free media and PCR amplification of the nifH genes. Streaking of the 432 isolates on nitrogen-rich R2A revealed many cocultures. In most cases, only one community member then grew on NFA, indicating the coexistence of nonfixers in coculture with fixers when growing under nitrogen-limited conditions. To exclude isolates able to scavenge residual nitrogen, such as that from vitamins, we used a stringent nitrogen-free medium containing only 6.42 μmol/L total nitrogen and recultured them in a nitrogen-depleted atmosphere. Surprisingly, PCR amplification of nifH using various primer pairs yielded amplicons from only 17% of the 442 isolates. The majority of the nifH PCR-negative isolates were Bacillus and Streptomyces. It is unclear whether these isolates have highly effective uptake systems or nitrogen reduction systems that are not closely aligned with known nitrogenase families. We advise caution in determining the nitrogen fixation ability of plants from growth on nitrogen-free media, even where the total nitrogen is very limited.

Revealing the size effect mechanisms of micro(nano)plastics on nitrogen removal performance of constructed wetland

Micro(nano)plastics (MPs) in aquatic environments can disrupt wastewater treatment, particularly nitrogen removal in constructed wetlands (CWs). However, their broader effects on microbial and plant nitrogen metabolism remain unclear. This study investigated the effects of different-sized MPs (4 mm, 100 µm, and 100 nm) on nitrogen transformation in CWs. Results revealed that 4 mm- and 100 µm-MPs did not significantly affect total nitrogen (TN) removal, although 100 µm-MPs significantly increased leaf antioxidant enzyme activities and reduced plant uptake of nitrogen by 12.95 % (p < 0.05). In contrast, 100 nm-MPs decreased the TN removal efficiency by 7.97 % via inhibiting both nitrification and denitrification, since 100 nm-MPs penetrated cell membranes, disrupted reactive oxygen species balance, and reduced bacterial viability, thus suppressing microbial nitrogen degradation by 8.07 % (p < 0.05). Additionally, 100 nm-MPs significantly inhibited plant growth and reduced plant nitrogen uptake by 16.05 % (p < 0.05). Furthermore, 100 µm-MPs increased the abundance of nitrifiers but reduced denitrifiers and functional genes, whereas 100 nm-MPs reduced the abundance of both nitrifiers and denitrifiers along with their functional genes (p < 0.05). These findings highlight the need to improve waste management to mitigate the adverse effects of MPs on nitrogen removal.

Temporal dynamics of the diazotrophic community during corpse decomposition

Corpse decomposition affects soil organisms through the formation of "cadaver decomposition islands." Soil diazotrophic microbes possess essential ecological functions on nitrogen input and nutrient cycling in the terrestrial ecosystem. However, our knowledge about how soil diazotrophic communities respond to corpse decomposition is lacking. In this study, we focused on the succession patterns and biological interaction of nitrogen-fixing microorganisms during animal (Ochotona curzoniae) corpse decomposition in terrestrial ecosystems by targeting nifH gene with high-throughput sequencing. Our results revealed that corpse decomposition of pikas reduced the α diversity and significantly impacted the β diversity of diazotrophic community across different decomposition stages. The divergent succession of diazotrophic community occurred under corpse pressure. Furthermore, the relative importance of stochasticity to the community assembly was improved by corpse decomposition, while the importance decreased over decomposition time. Cadaver decay also simplified the diazotrophic networks and weakened the biological interactions among diazotrophic populations. Notably, NH4-N was the most important factor affecting diazotrophic community, followed by time and total carbon. This work emphasized that corpse decomposition perhaps influences the process of biological nitrogen fixation by altering soil diazotrophic communities, which is of great significance for understanding the terrestrial ecosystems' nitrogen cycle functions. KEY POINTS: • Corpse decomposition reduced the α diversity of diazotrophic community. • Corpse decomposition improved the stochasticity of diazotrophic community assembly. • Corpse decomposition weakened the interactions among diazotrophic populations.

Microbial genetic potential differs among cryospheric habitats of the Damma glacier

Climate warming has led to glacier retreat worldwide. Studies on the taxonomy and functions of glacier microbiomes help us better predict their response to glacier melting. Here, we used shotgun metagenomic sequencing to study the microbial functional potential in different cryospheric habitats, i.e. surface snow, supraglacial and subglacial sediments, subglacial ice, proglacial stream water and recently deglaciated soils. The functional gene structure varied greatly among habitats, especially for snow, which differed significantly from all other habitats. Differential abundance analysis revealed that genes related to stress responses (e.g. chaperones) were enriched in ice habitat, supporting the fact that glaciers are a harsh environment for microbes. The microbial metabolic capabilities related to carbon and nitrogen cycling vary among cryospheric habitats. Genes related to auxiliary activities were overrepresented in the subglacial sediment, suggesting a higher genetic potential for the degradation of recalcitrant carbon (e.g., lignin). As for nitrogen cycling, genes related to nitrogen fixation were more abundant in barren proglacial soils, possibly due to the presence of Cyanobacteriota in this habitat. Our results deepen our understanding of microbial processes in glacial ecosystems, which are vulnerable to ongoing global warming, and they have implications for downstream ecosystems.

Mechanism of microbial action of the inoculated nitrogen-fixing bacterium for growth promotion and yield enhancement in rice (Oryza sativa L.)

The use of nitrogen-fixing bacteria in agriculture is increasingly recognized as a sustainable method to boost crop yields, reduce chemical fertilizer use, and improve soil health. However, the microbial mechanisms by which inoculation with nitrogen-fixing bacteria enhance rice production remain unclear. In this study, rice seedlings were inoculated with the nitrogen-fixing bacterium R3 (Herbaspirillum) at the rhizosphere during the seedling stage in a pot experiment using paddy soil. We investigated the effects of such inoculation on nutrient content in the rhizosphere soil, plant growth, and the nitrogen-fixing microbial communities within the rhizosphere and endorhizosphere. The findings showed that inoculation with the R3 strain considerably increased the amounts of nitrate nitrogen, ammonium nitrogen, and available phosphorus in the rhizosphere by 14.77%, 27.83%, and 22.67%, respectively, in comparison to the control (CK). Additionally, the theoretical yield of rice was enhanced by 8.81% due to this inoculation, primarily through a 10.24% increase in the effective number of rice panicles and a 4.14% increase in the seed setting rate. Further analysis revealed that the structure of the native nitrogen-fixing microbial communities within the rhizosphere and endorhizosphere were altered by inoculation with the R3 strain, significantly increasing the α-diversity of the communities. The relative abundance of key nitrogen-fixing genera such as Ralstonia, Azotobacter, Geobacter, Streptomyces, and Pseudomonas were increased, enhancing the quantity and community stability of the nitrogen-fixing community. Consequently, the nitrogen-fixing capacity and sustained activity of the microbial community in the rhizosphere soil were strengthened. Additionally, the expression levels of the nitrogen absorption and transport-related genes OsNRT1 and OsPTR9 in rice roots were upregulated by inoculation with the R3 strain, potentially contributing to the increased rice yield. Our study has revealed the potential microbial mechanisms through which inoculation with nitrogen-fixing bacteria enhances rice yield. This finding provides a scientific basis for subsequent agricultural practices and is of critical importance for increasing rice production and enhancing the ecosystem services of rice fields.

Eddy-driven diazotroph distribution in the subtropical North Atlantic: horizontal variability prevails over particle sinking speed

Mesoscale eddies influence the distribution of diazotrophic (nitrogen-fixing) cyanobacteria, impacting marine productivity and carbon export. Non-cyanobacterial diazotrophs (NCDs) are emerging as potential contributors to marine nitrogen fixation, relying on organic matter particles for resources, impacting nitrogen and carbon cycling. However, their diversity and biogeochemical importance remain poorly understood. In the subtropical North Atlantic along a single transect, this study explored the horizontal and vertical spatial variability of NCDs associated with suspended, slow-sinking, and fast-sinking particles collected with a marine snow catcher. The investigation combined amplicon sequencing with hydrographic and biogeochemical data. Cyanobacterial diazotrophs and NCDs were equally abundant, and their diversity was explained by the structure of the eddy. The unicellular symbiotic cyanobacterium UCYN-A was widespread across the eddy, whereas Trichodesmium and Crocosphaera accumulated at outer fronts. The diversity of particle-associated NCDs varied more horizontally than vertically. NCDs constituted most reads in the fast-sinking fractions, mainly comprising Alphaproteobacteria, whose abundance significantly differed from the suspended and slow-sinking fractions. Horizontally, Gammaproteobacteria and Betaproteobacteria exhibited inverse distributions, influenced by physicochemical characteristics of water intrusions at the eddy periphery. Niche differentiations across the anticyclonic eddy underscored NCD-particle associations and mesoscale dynamics, deepening our understanding of their ecological role and impact on ocean biogeochemistry.

Employment of pqqE gene as molecular marker for the traceability of Gram negative phosphate solubilizing bacteria associated to plants

Insoluble phosphorous compounds solubilization by soil bacteria is of great relevance since it puts available the phosphorus to be used by plants. The production of organic acids is the main microbiological mechanism by which insoluble inorganic phosphorus compounds are solubilized. In Gram negative bacteria, gluconic acid is synthesized by the activity of the holoenzyme glucose dehydrogenase-pyrroloquinoline quinine named GDH-PQQ. The use of marker genes is a very useful tool to evaluate the persistence of the introduced bacteria and allow to follow-up the effect of biotic and abiotic factors on these beneficial microorganisms in the soil. In previous studies we detected the presence of the pqqE gene in a great percentage of both non-culturable and culturable native soil bacteria. The objective of this study was to analyze the phylogeny of the sequence of pqqE gene and its potential for the study of phosphate solubilizing bacteria from pure and mixed bacterial cultures and rhizospheric soil samples. For this, the presence of the pqqE gene in the genome of phosphate solubilizing bacteria that belong to several bacteria was determined by PCR. Also, this gene was analyzed from mixed bacterial cultures and rhizospheric soil associated to peanut plants inoculated or not with phosphate solubilizing bacteria. For this, degenerate primers designed from several bacterial genera and specific primers for the genus Pseudomonas spp., designed in this study, were used. DNA template used from simple or mixed bacterial cultures and from rhizospheric soil samples was obtained using two different DNA extraction techniques. Results indicated that pqqE gene amplification product was found in the genome of all Gram negative phosphate solubilizing bacteria analyzed. It was possible to detect this gene in the DNA obtained from mixed cultures where these bacteria grew in interaction with other microorganisms and in that obtained from rhizospheric soil samples inoculated or not with these bacteria. The phylogenetic analysis indicated that pqqE gene is a conserved gene within related genera. In conclusion, pqqE gene could be a potential marker for the study of phosphate solubilizing bacterial populations.

Endophytic diazotrophic communities from rice roots are diverse and weakly associated with soil diazotrophic community composition and soil properties

AIM

Bacteria that promote plant growth, such as diazotrophs, are valuable tools for achieving a more sustainable production of important non-legume crops like rice. Different strategies have been used to discover new bacteria capable of promoting plant growth. This work evaluated the contribution of soil diazotrophs to the endophytic communities established in the roots of rice seedlings cultivated on seven representative soils from Uruguay.

METHODS AND RESULTS

The soils were classified into two groups according to the C and clay content. qPCR, terminal restriction fragment length polymorphism (T-RFLP), and 454-pyrosequencing of the nifH gene were used for analyzing diazotrophs in soil and plantlets' roots grown from seeds of the same genotype for 25 days under controlled conditions. A similar nifH abundance was found among the seven soils, roots, or leaves. The distribution of diazotrophs was more uneven in roots than in soils, with dominance indices significantly higher than in soils (nifH T-RFLP). Dominant soils' diazotrophs were mainly affiliated to Alphaproteobacteria and Planctomycetota. Conversely, Alpha, Beta, Gammaproteobacteria, and Bacillota were predominant in different roots, though undetectable in soils. Almost no nifH sequences were shared between soils and roots.

CONCLUSIONS

Root endophytic diazotrophs comprised a broader taxonomic range of microorganisms than diazotrophs found in soils from which the plantlets were grown and showed strong colonization patterns.

Epiphytic Bacterial Community Analysis of Ulva prolifera in Garorim and Muan Bays, Republic of Korea

The bacterial communities related to seaweed can vary considerably across different locations, and these variations influence the seaweed's nutrition, growth, and development. To study this further, we evaluated the bacteria found on the green marine seaweed Ulva prolifera from Garorim Bay and Muan Bay, two key locations on Republic of Korea's west coast. Our analysis found notable differences in the bacterial communities between the two locations. Garorim Bay hosted a more diverse bacterial population, with the highest number of ASVs (871) compared to Muan Bay's 156 ASVs. In Muan Bay, more than 50% of the bacterial community was dominated by Pseudomonadota. On the other hand, Garorim Bay had a more balanced distribution between Bacteroidota and Pseudomonadota (37% and 35.5%, respectively). Additionally, Cyanobacteria, particularly Cyanothece aeruginosa, were found in significant numbers in Garorim Bay, making up 8% of the community. Mineral analysis indicated that Garorim Bay had higher levels of S, Na, Mg, Ca, and Fe. Function-wise, both locations exhibited bacterial enrichment in amino acid production, nucleosides, and nucleotide pathways. In conclusion, this study broadens our understanding of the bacterial communities associated with Ulva prolifera in Korean waters and provides a foundation for future research on the relationships between U. prolifera and its bacteria.

Discovery of Eremiobacterota with nifH homologues in tundra soil

We describe the genome of an Eremiobacterota population from tundra soil that contains the minimal set of nif genes needed to fix atmospheric N2. This putative diazotroph population, which we name Candidatus Lamibacter sapmiensis, links for the first time Eremiobacterota and N2 fixation. The integrity of the genome and its nif genes are well supported by both environmental and taxonomic signals. Ca. Lamibacter sapmiensis contains three nifH homologues and the complementary set of nifDKENB genes that are needed to assemble a functional nitrogenase. The putative diazotrophic role of Ca. Lamibacter sapmiensis is supported by the presence of genes that regulate N2 fixation and other genes involved in downstream processes such as ammonia assimilation. Similar to other Eremiobacterota, Ca. Lamibacter sapmiensis encodes the potential for atmospheric chemosynthesis via CO2 fixation coupled with H2 and CO oxidation. Interestingly, the presence of a N2O reductase indicates that this population could play a role as a N2O sink in tundra soils. Due to the lack of activity data, it remains uncertain if Ca. Lamibacter sapmiensis is able to assemble a functional nitrogenase and participate in N2 fixation. Confirmation of this ability would be a testament to the great metabolic versatility of Eremiobacterota, which appears to underlie their ecological success in cold and oligotrophic environments.

Enhancing boreal forest resilience: A four-year impact of biochar on soil quality and fungal communities

Boreal forests commonly suffer from nutrient deficiency due to restricted biological activity and decomposition. Biochar has been used as a promising strategy to improve soil quality, yet its impacts on forest soil microbes, particularly in cold environment, remains poorly understood. In this study, we investigated the effects of biochar, produced at different pyrolysis temperatures (500 °C and 650 °C) and applied at different amounts (0.5 kg·m-2 and 1.0 kg·m-2), on soil property, soil enzyme activity, and fungal community dynamics in a boreal forest over a span of two to four years. Our results showed that, four-year post-application of biochar produced at 650 °C and applied at 1.0 kg·m-2, significantly increased the relative abundance of Mortierellomycota and enhanced fungal species richness, α-diversity and evenness compared to the control (CK) (P < 0.05). Notably, the abundance of Phialocephala fortinii increased with the application of biochar produced at 500 °C and applied at 0.5 kg·m-2, exhibiting a positively correlation with the carbon cycling-related enzyme β-cellobiosidase. Functionally, distinct fungal gene structures were formed between different biochar pyrolysis temperatures, and between application amounts in four-year post-biochar application (P < 0.05). Additionally, correlation analyses revealed the significance of the duration post-biochar application on the soil properties, soil extracellular enzymes, soil fungal dominant phyla, fungal community and gene structures (P < 0.01). The interaction between biochar pyrolysis temperature and application amount significantly influenced fungal α-diversity (P < 0.01). Overall, these findings provide theoretical insights and practical application for biochar as soil amendment in boreal forest ecosystems.

Physiological response of mussel to rayon microfibers and PCB's exposure: Overlooked semi-synthetic micropollutant?

Rayon microfibers, micro-sized semi-synthetic polymers derived from cellulose, have been frequently detected and reported as "micropollutants" in marine environments. However, there has been limited research on their ecotoxicity and combined effects with persistent organic pollutants (POPs). To address these knowledge gaps, thick-shell mussels (Mytilus coruscus) were exposed to rayon microfibers at 1000 pieces/L, along with polychlorinated biphenyls (PCBs) at 100 and 1000 ng/L for 14 days, followed by a 7-day recovery period. We found that rayon microfibers at the environmentally relevant concentration exacerbated the irreversible effects of PCBs on the immune and digestive systems of mussels, indicating chronic and sublethal impacts. Furthermore, the results of 16 s rRNA sequencing demonstrated significant effects on the community structure, species richness, and diversity of the mussels' intestinal microbiota. The branching map analysis identified the responsive bacteria to rayon microfibers and PCBs belonging to the Proteobacteria, Actinobacteriota, and Bacteroidota phyla. Despite not being considered a conventional plastic, the extensive and increasing use of rayon fibers, their direct toxicological effects, and their interaction with POPs highlight the need for urgent attention, investigation, and regulation to address their contribution to "micropollution".

Agronomic advantage of bacterial biological nitrogen fixation on wheat plant growth under contrasting nitrogen and phosphorus regimes

Introduction

Given their remarkable capacity to convert atmospheric nitrogen into plant-accessible ammonia, nitrogen-fixing microbial species hold promise as a sustainable alternative to chemical nitrogen fertilizers, particularly in economically significant crops like wheat. This study aimed to identify strains with optimal attributes for promoting wheat growth sustainably, with a primary emphasis on reducing reliance on chemical nitrogen fertilizers.

Methods

We isolated free nitrogen-fixing strains from diverse rhizospheric soils across Morocco. Subsequently, we conducted a rigorous screening process to evaluate their plant growth-promoting traits, including nitrogen fixation, phosphate solubilization, phytohormone production and their ability to enhance wheat plant growth under controlled conditions. Two specific strains, Rhodotorula mucilaginosa NF 516 and Arthrobacter sp. NF 528, were selected for in-depth evaluation, with the focus on their ability to reduce the need for chemical nitrogen supply, particularly when used in conjunction with TSP fertilizer and natural rock phosphate. These two sources of phosphate were chosen to assess their agricultural effectiveness on wheat plants.

Results and discussion

Twenty-two nitrogen-fixing strains (nif-H+) were isolated from various Moroccan rhizospheric soils, representing Bacillus sp., Pseudomonas sp., Arthrobacter sp., Burkholderia sp. and a yeast-like microorganism. These strains were carefully selected based on their potential to promote plant growth. The findings revealed that the application of Rhodotorula mucilaginosa NF 516 and Arthrobacter sp. NF 528 individually or in combination, significantly improved wheat plant growth and enhanced nutrients (N and P) uptake under reduced nitrogen regimes. Notably, their effectiveness was evident in response to both natural rock phosphate and TSP, demonstrating their important role in wheat production under conditions of low nitrogen and complex phosphorus inputs. This research underscores the significant role of nitrogen-fixing microorganisms, particularly Rhodotorula mucilaginosa NF 516 and Arthrobacter sp. NF 528, in wheat production under conditions of low nitrogen and complex phosphorus inputs. It showcases their potential to reduce chemical nitrogen fertilization requirements by up to 50% without compromising wheat plant yields. Our study emphasizes the importance of bacterial biological nitrogen fixation in meeting the remaining nitrogen requirements beyond this reduction. This underscores the vital role of microbial contributions in providing essential nitrogen for optimal plant growth and highlights the significance of biological nitrogen fixation in sustainable agriculture practices.

The prokaryotic and eukaryotic microbiome of Pacific oyster spat is shaped by ocean warming but not acidification

Pacific oysters (Magallana gigas, a.k.a. Crassostrea gigas), the most widely farmed oysters, are under threat from climate change and emerging pathogens. In part, their resilience may be affected by their microbiome, which, in turn, may be influenced by ocean warming and acidification. To understand these impacts, we exposed early-development Pacific oyster spat to different temperatures (18°C and 24°C) and pCO2 levels (800, 1,600, and 2,800 µatm) in a fully crossed design for 3 weeks. Under all conditions, the microbiome changed over time, with a large decrease in the relative abundance of potentially pathogenic ciliates (Uronema marinum) in all treatments with time. The microbiome composition differed significantly with temperature, but not acidification, indicating that Pacific oyster spat microbiomes can be altered by ocean warming but is resilient to ocean acidification in our experiments. Microbial taxa differed in relative abundance with temperature, implying different adaptive strategies and ecological specializations among microorganisms. Additionally, a small proportion (~0.2% of the total taxa) of the relatively abundant microbial taxa were core constituents (>50% occurrence among samples) across different temperatures, pCO2 levels, or time. Some taxa, including A4b bacteria and members of the family Saprospiraceae in the phyla Chloroflexi (syn. Chloroflexota) and Bacteroidetes (syn. Bacteroidota), respectively, as well as protists in the genera Labyrinthula and Aplanochytrium in the class Labyrinthulomycetes, and Pseudoperkinsus tapetis in the class Ichthyosporea were core constituents across temperatures, pCO2 levels, and time, suggesting that they play an important, albeit unknown, role in maintaining the structural and functional stability of the Pacific oyster spat microbiome in response to ocean warming and acidification. These findings highlight the flexibility of the spat microbiome to environmental changes.IMPORTANCEPacific oysters are the most economically important and widely farmed species of oyster, and their production depends on healthy oyster spat. In turn, spat health and productivity are affected by the associated microbiota; yet, studies have not scrutinized the effects of temperature and pCO2 on the prokaryotic and eukaryotic microbiomes of spat. Here, we show that both the prokaryotic and, for the first time, eukaryotic microbiome of Pacific oyster spat are surprisingly resilient to changes in acidification, but sensitive to ocean warming. The findings have potential implications for oyster survival amid climate change and underscore the need to understand temperature and pCO2 effects on the microbiome and the cascading effects on oyster health and productivity.

Seagrass-mediated rhizosphere redox gradients are linked with ammonium accumulation driven by diazotrophs

Seagrasses can enhance nutrient mobilization in their rhizosphere via complex interactions with sediment redox conditions and microbial populations. Yet, limited knowledge exists on how seagrass-derived rhizosphere dynamics affect nitrogen cycling. Using optode and gel-sampler-based chemical imaging, we show that radial O2 loss (ROL) from rhizomes and roots leads to the formation of redox gradients around below-ground tissues of seagrass (Zostera marina), which are co-localized with regions of high ammonium concentrations in the rhizosphere. Combining such chemical imaging with fine-scale sampling for microbial community and gene expression analyses indicated that multiple biogeochemical pathways and microbial players can lead to high ammonium concentration within the oxidized regions of the seagrass rhizosphere. Symbiotic N2-fixing bacteria (Bradyrhizobium) were particularly abundant and expressed the diazotroph functional marker gene nifH in Z. marina rhizosphere areas with high ammonium concentrations. Such an association between Z. marina and Bradyrhizobium can facilitate ammonium mobilization, the preferred nitrogen source for seagrasses, enhancing seagrass productivity within nitrogen-limited environments. ROL also caused strong gradients of sulfide at anoxic/oxic interfaces in rhizosphere areas, where we found enhanced nifH transcription by sulfate-reducing bacteria. Furthermore, we found a high abundance of methylotrophic and sulfide-oxidizing bacteria in rhizosphere areas, where O2 was released from seagrass rhizomes and roots. These bacteria could play a beneficial role for the plants in terms of their methane and sulfide oxidation, as well as their formation of growth factors and phytohormones. ROL from below-ground tissues of seagrass, thus, seems crucial for ammonium production in the rhizosphere via stimulation of multiple diazotrophic associations.

IMPORTANCE

Seagrasses are important marine habitats providing several ecosystem services in coastal waters worldwide, such as enhancing marine biodiversity and mitigating climate change through efficient carbon sequestration. Notably, the fitness of seagrasses is affected by plant-microbe interactions. However, these microscale interactions are challenging to study and large knowledge gaps prevail. Our study shows that redox microgradients in the rhizosphere of seagrass select for a unique microbial community that can enhance the ammonium availability for seagrass. We provide first experimental evidence that Rhizobia, including the symbiotic N2-fixing bacteria Bradyrhizobium, can contribute to the bacterial ammonium production in the seagrass rhizosphere. The release of O2 from rhizomes and roots also caused gradients of sulfide in rhizosphere areas with enhanced nifH transcription by sulfate-reducing bacteria. O2 release from seagrass root systems thus seems crucial for ammonium production in the rhizosphere via stimulation of multiple diazotrophic associations.

Pontiella agarivorans sp. nov., a novel marine anaerobic bacterium capable of degrading macroalgal polysaccharides and fixing nitrogen

Marine macroalgae produce abundant and diverse polysaccharides, which contribute substantially to the organic matter exported to the deep ocean. Microbial degradation of these polysaccharides plays an important role in the turnover of macroalgal biomass. Various members of the Planctomycetes-Verrucomicrobia-Chlamydia (PVC) superphylum are degraders of polysaccharides in widespread anoxic environments. In this study, we isolated a novel anaerobic bacterial strain NLcol2T from microbial mats on the surface of marine sediments offshore Santa Barbara, CA, USA. Based on 16S ribosomal RNA (rRNA) gene and phylogenomic analyses, strain NLcol2T represents a novel species within the Pontiella genus in the Kiritimatiellota phylum (within the PVC superphylum). Strain NLcol2T is able to utilize various monosaccharides, disaccharides, and macroalgal polysaccharides such as agar and ɩ-carrageenan. A near-complete genome also revealed an extensive metabolic capacity for anaerobic degradation of sulfated polysaccharides, as evidenced by 202 carbohydrate-active enzymes (CAZymes) and 165 sulfatases. Additionally, its ability of nitrogen fixation was confirmed by nitrogenase activity detected during growth on nitrogen-free medium, and the presence of nitrogenases (nifDKH) encoded in the genome. Based on the physiological and genomic analyses, this strain represents a new species of bacteria that may play an important role in the degradation of macroalgal polysaccharides and with relevance to the biogeochemical cycling of carbon, sulfur, and nitrogen in marine environments. Strain NLcol2T (= DSM 113125T = MCCC 1K08672T) is proposed to be the type strain of a novel species in the Pontiella genus, and the name Pontiella agarivorans sp. nov. is proposed.IMPORTANCEGrowth and intentional burial of marine macroalgae is being considered as a carbon dioxide reduction strategy but elicits concerns as to the fate and impacts of this macroalgal carbon in the ocean. Diverse heterotrophic microbial communities in the ocean specialize in these complex polymers such as carrageenan and fucoidan, for example, members of the Kiritimatiellota phylum. However, only four type strains within the phylum have been cultivated and characterized to date, and there is limited knowledge about the metabolic capabilities and functional roles of related organisms in the environment. The new isolate strain NLcol2T expands the known substrate range of this phylum and further reveals the ability to fix nitrogen during anaerobic growth on macroalgal polysaccharides, thereby informing the issue of macroalgal carbon disposal.

Effects of elevated temperature and different crystal structures of TiO2 nanoparticles on the gut microbiota of mussel Mytilus coruscus

Coastal habitats are exposed to increasing pressure of nanopollutants commonly combined with warming due to the seasonal temperature cycles and global climate change. To investigate the toxicological effects of TiO2 nanoparticles (TiO2 NPs) and elevated temperature on the intestinal health of the mussels (Mytilus coruscus), the mussels were exposed to 0.1 mg/L TiO2 NPs with different crystal structures for 14 days at 20 °C and 28 °C, respectively. Compared to 20 °C, the agglomeration of TiO2 NPs was more serious at 28 °C. Exposure to TiO2 NPs led to elevated mortality of M. coruscus and modified the intestinal microbial community as shown by 16S rRNA sequence analysis. Exposure to TiO2 NPs changed the relative abundance of Bacteroidetes, Proteobacteria and Firmicutes. The relative abundances of putative mutualistic symbionts Tenericutes and Fusobacteria increased in the gut of M. coruscus exposed to anatase, which have contributed to the lower mortality in this group. LEfSe showed the combined stress of warming and TiO2 NPs increased the risk of M. coruscus being infected with potential pathogenic bacteria. This study emphasizes the toxicity differences between crystal structures of TiO2 NPs, and will provides an important reference for analyzing the physiological and ecological effects of nanomaterial pollution on bivalves under the background of global climate change.

Gut diazotrophs in lagomorphs are associated with season but not altitude and host phylogeny

Invertebrates such as termites feeding on nutrient-poor substrate receive essential nitrogen by biological nitrogen fixation of gut diazotrophs. However, the diversity and composition of gut diazotrophs of vertebrates such as Plateau pikas living in nutrient-poor Qinghai-Tibet Plateau remain unknown. To fill this knowledge gap, we studied gut diazotrophs of Plateau pikas (Ochotona curzoniae) and its related species, Daurian pikas (Ochotona daurica), Hares (Lepus europaeus) and Rabbits (Oryctolagus cuniculus) by high-throughput amplicon sequencing methods. We analyzed whether the gut diazotrophs of Plateau pikas are affected by season, altitude, and species, and explored the relationship between gut diazotrophs and whole gut microbiomes. Our study showed that Firmicutes, Spirochaetes, and Euryarchaeota were the dominant gut diazotrophs of Plateau pikas. The beta diversity of gut diazotrophs of Plateau pikas was significantly different from the other three lagomorphs, but the alpha diversity did not show a significant difference among the four lagomorphs. The gut diazotrophs of Plateau pikas were the most similarly to that of Rabbits, followed by Daurian pikas and Hares, which was inconsistent with gut microbiomes or animal phylogeny. The dominant gut diazotrophs of the four lagomorphs may reflect their living environment and dietary habits. Season significantly affected the alpha diversity and abundance of dominant gut diazotrophs. Altitude had no significant effect on the gut diazotrophs of Plateau pikas. In addition, the congruence between gut microbiomes and gut diazotrophs was low. Our results proved that the gut of Plateau pikas was rich in gut diazotrophs, which is of great significance for the study of ecology and evolution of lagomorphs.

Chemolithoautotrophic diazotrophs dominate dark nitrogen fixation in mangrove sediments

Diazotrophic microorganisms regulate marine productivity by alleviating nitrogen limitation. So far chemolithoautotrophic bacteria are widely recognized as the principal diazotrophs in oligotrophic marine and terrestrial ecosystems. However, the contribution of chemolithoautotrophs to nitrogen fixation in organic-rich habitats remains unclear. Here, we utilized metagenomic and metatranscriptomic approaches integrated with cultivation assays to investigate the diversity, distribution, and activity of diazotrophs residing in Zhangzhou mangrove sediments. Physicochemical assays show that the studied mangrove sediments are typical carbon-rich, sulfur-rich, nitrogen-limited, and low-redox marine ecosystems. These sediments host a wide phylogenetic variety of nitrogenase genes, including groups I-III and VII-VIII. Unexpectedly diverse chemolithoautotrophic taxa including Campylobacteria, Gammaproteobacteria, Zetaproteobacteria, and Thermodesulfovibrionia are the predominant and active nitrogen fixers in the 0-18 cm sediment layer. In contrast, the 18-20 cm layer is dominated by active diazotrophs from the chemolithoautotrophic taxa Desulfobacterota and Halobacteriota. Further analysis of MAGs shows that the main chemolithoautotrophs can fix nitrogen by coupling the oxidation of hydrogen, reduced sulfur, and iron, with the reduction of oxygen, nitrate, and sulfur. Culture experiments further demonstrate that members of chemolithoautotrophic Campylobacteria have the nitrogen-fixing capacity driven by hydrogen and sulfur oxidation. Activity measurements confirm that the diazotrophs inhabiting mangrove sediments preferentially drain energy from diverse reduced inorganic compounds other than from organics. Overall, our results suggest that chemolithoautotrophs rather than heterotrophs are dominant nitrogen fixers in mangrove sediments. This study underscores the significance of chemolithoautotrophs in carbon-dominant ecosystems.

Diazotrophic abundance and community structure associated with three meadow plants on the Qinghai-Tibet Plateau

Symbiotic diazotrophs form associations with legumes and substantially fix nitrogen into soils. However, grasslands on the Qinghai-Tibet Plateau are dominated by non-legume plants, such as Kobresia tibetica. Herein, we investigated the diazotrophic abundance, composition, and community structure in the soils and roots of three plants, non-legume K. tibetica and Kobresia humilis and the legume Oxytropis ochrocephala, using molecular methods targeting nifH gene. Diazotrophs were abundantly observed in both bulk and rhizosphere soils, as well as in roots of all three plants, but their abundance varied with plant type and soil. In both bulk and rhizosphere soils, K. tibetica showed the highest diazotroph abundance, whereas K. humilis had the lowest. In roots, O. ochrocephala and K. humilis showed the highest and the lowest diazotroph abundance, respectively. The bulk and rhizosphere soils exhibited similar diazotrophic community structure in both O. ochrocephala and K. tibetica, but were substantially distinct from the roots in both plants. Interestingly, the root diazotrophic community structures in legume O. ochrocephala and non-legume K. tibetica were similar. Diazotrophs in bulk and rhizosphere soils were more diverse than those in the roots of three plants. Rhizosphere soils of K. humilis were dominated by Actinobacteria, while rhizosphere soils and roots of K. tibetica were dominated by Verrumicrobia and Proteobacteria. The O. ochrocephala root diazotrophs were dominated by Alphaproteobacteria. These findings indicate that free-living diazotrophs abundantly and diversely occur in grassland soils dominated by non-legume plants, suggesting that these diazotrophs may play important roles in fixing nitrogen into soils on the plateau.

Seasonal dynamics of phyllosphere epiphytic microbial communities of medicinal plants in farmland environment

Introduction

The phyllosphere of plants is inhabited by various microorganisms, which play a crucial role in plant physiological metabolism. Currently, there is limited research on the dynamic effects of species and seasons on plant phyllosphere microbial community diversity and microbial interactions.

Methods

In this study, high-throughput sequencing technology was used to sequence the leaf surface parasitic microorganisms of five medicinal plants (Bupleurum chinense, Atractylodes lancea, Salvia miltiorrhiza, Astragalus membranaceus, and Lonicera japonica).

Results

The results showed that bacteria and fungi clustered into 3,898 and 1,572 operational taxonomic units (OTUs), respectively. Compared to host species, seasons had a more significant impact on the a diversity of bacteria and fungi. The heterogeneity of phyllosphere microbial communities was greater in winter compared to summer. Key species analysis at the OTU level and Spearman correlation analysis demonstrated significant preferences in microbial interactions under plant and seasonal backgrounds. The network connections between bacterial and fungal communities significantly increased during seasonal transitions compared to connections with plants.

Discussion

This study enhances our understanding of the composition and ecological roles of plant-associated microbial communities in small-scale agricultural environments. Additionally, it provides valuable insights for assessing the biodiversity of medicinal plants.

Effects of Cascade Reservoirs on Spatiotemporal Dynamics of the Sedimentary Bacterial Community: Co-occurrence Patterns, Assembly Mechanisms, and Potential Functions

Dam construction as an important anthropogenic activity significantly influences ecological processes in altered freshwater bodies. However, the effects of multiple cascade dams on microbial communities have been largely overlooked. In this study, the spatiotemporal distribution, co-occurrence relationships, assembly mechanisms, and functional profiles of sedimentary bacterial communities were systematically investigated in 12 cascade reservoirs across two typical karst basins in southwest China over four seasons. A significant spatiotemporal heterogeneity was observed in bacterial abundance and diversity. Co-occurrence patterns in the Wujiang Basin exhibited greater edge counts, graph density, average degree, robustness, and reduced modularity, suggesting more intimate and stronger ecological interactions among species than in the Pearl River Basin. Furthermore, Armatimonadota and Desulfobacterota, identified as keystone species, occupied a more prominent niche than the dominant species. A notable distance-decay relationship between geographical distance and community dissimilarities was identified in the Pearl River Basin. Importantly, in the Wujiang Basin, water temperature emerged as the primary seasonal variable steering the deterministic process of bacterial communities, whereas 58.5% of the explained community variance in the neutral community model (NCM) indicated that stochastic processes governed community assembly in the Pearl River Basin. Additionally, principal component analysis (PCA) revealed more pronounced seasonal dynamics in nitrogen functional compositions than spatial variation in the Wujiang Basin. Redundancy analysis (RDA) results indicated that in the Wujiang Basin, environmental factors and in Pearl River Basin, geographical distance, reservoir age, and hydraulic retention time (HRT), respectively, influenced the abundance of nitrogen-related genes. Notably, these findings offer novel insights: building multiple cascade reservoirs could lead to a cascading decrease in biodiversity and resilience in the river-reservoir ecosystem.

Oyster aquaculture enhances sediment microbial diversity- Insights from a multi-omics study

The global aquaculture industry has grown substantially, with consequences for coastal ecology and biogeochemistry. Oyster aquaculture can alter the availability of resources for microbes that live in sediments as oysters move large quantities of organic material to the sediments via filter feeding, possibly leading to changes in the structure and function of sediment microbial communities. Here, we use a chronosequence approach to investigate the impacts of oyster farming on sediment microbial communities over 7 years of aquaculture activity in a temperate coastal system. We detected shifts in bacterial composition (16S rRNA amplicon sequencing), changes in gene expression (meta-transcriptomics), and variations in sediment elemental concentrations (sediment geochemistry) across different durations of oyster farming. Our results indicate that both the structure and function of bacterial communities vary between control (no oysters) and farm sites, with an overall increase in diversity and a shift towards anoxic tolerance in farm sites. However, little to no variation was observed in either structure or function with respect to farming duration suggesting these sediment microbial communities are resilient to change. We also did not find any significant impact of farming on heavy metal accumulation in the sediments. The minimal influence of long-term oyster farming on sediment bacterial function and biogeochemical processes as observed here can bear important consequences for establishing best practices for sustainable farming in these areas.

Importance

Sediment microbial communities drive a range of important ecosystem processes such as nutrient recycling and filtration. Oysters are well-known ecological engineers, and their presence is increasing as aquaculture expands in coastal waters globally. Determining how oyster aquaculture impacts sediment microbial processes is key to understanding current and future estuarine biogeochemical processes. Here, we use a multi-omics approach to study the effect of different durations of oyster farming on the structure and function of bacteria and elemental accumulation in the farm sediments. Our results indicate an increase in the diversity of bacterial communities in the farm sites with no such increases observed for elemental concentrations. Further, these effects persist across multiple years of farming with an increase of anoxic tolerant bacteria at farm sites. The multi-omics approach used in this study can serve as a valuable tool to facilitate understanding of the environmental impacts of oyster aquaculture.

Marine nitrogen-fixers in the Canadian Arctic Gateway are dominated by biogeographically distinct noncyanobacterial communities

We describe diazotrophs present during a 2015 GEOTRACES expedition through the Canadian Arctic Gateway (CAG) using nifH metabarcoding. In the less studied Labrador Sea, Bradyrhizobium sp. and Vitreoscilla sp. nifH variants were dominant, while in Baffin Bay, a Stutzerimonas stutzeri variant was dominant. In comparison, the Canadian Arctic Archipelago (CAA) was characterized by a broader set of dominant variants belonging to Desulfobulbaceae, Desulfuromonadales, Arcobacter sp., Vibrio spp., and Sulfuriferula sp. Although dominant diazotrophs fell within known nifH clusters I and III, only a few of these variants were frequently recovered in a 5-year weekly nifH times series in the coastal NW Atlantic presented herein, notably S. stutzeri and variants belonging to Desulfobacterales and Desulfuromonadales. In addition, the majority of dominant Arctic nifH variants shared low similarity (< 92% nucleotide identities) to sequences in a global noncyanobacterial diazotroph catalog recently compiled by others. We further detected UCYN-A throughout the CAG at low-levels using quantitative-PCR assays. Temperature, depth, salinity, oxygen, and nitrate were most strongly correlated to the Arctic diazotroph diversity observed, and we found a stark division between diazotroph communities of the Labrador Sea versus Baffin Bay and the CAA, hence establishing that a previously unknown biogeographic community division can occur for diazotrophs in the CAG.

Non-cyanobacterial diazotrophs: global diversity, distribution, ecophysiology, and activity in marine waters

Biological dinitrogen (N2) fixation supplies nitrogen to the oceans, supporting primary productivity, and is carried out by some bacteria and archaea referred to as diazotrophs. Cyanobacteria are conventionally considered to be the major contributors to marine N2 fixation, but non-cyanobacterial diazotrophs (NCDs) have been shown to be distributed throughout ocean ecosystems. However, the biogeochemical significance of marine NCDs has not been demonstrated. This review synthesizes multiple datasets, drawing from cultivation-independent molecular techniques and data from extensive oceanic expeditions, to provide a comprehensive view into the diversity, biogeography, ecophysiology, and activity of marine NCDs. A NCD nifH gene catalog was compiled containing sequences from both PCR-based and PCR-free methods, identifying taxa for future studies. NCD abundances from a novel database of NCD nifH-based abundances were colocalized with environmental data, unveiling distinct distributions and environmental drivers of individual taxa. Mechanisms that NCDs may use to fuel and regulate N2 fixation in response to oxygen and fixed nitrogen availability are discussed, based on a metabolic analysis of recently available Tara Oceans expedition data. The integration of multiple datasets provides a new perspective that enhances understanding of the biology, ecology, and biogeography of marine NCDs and provides tools and directions for future research.

Stochastic Processes Dominate in the Water Mass-Based Segregation of Diazotrophs in a High Arctic Fjord (Svalbard)

Nitrogen-fixing or diazotrophic microbes fix atmospheric nitrogen (N2) to ammonia (NH3+) using nitrogenase enzyme and play a crucial role in regulating marine primary productivity and carbon dioxide sequestration. However, there is a lack of information about the diversity, structure, and environmental regulations of the diazotrophic communities in the high Arctic fjords, such as Kongsfjorden. Here, we employed nifH gene sequencing to clarify variations in composition, community structure, and assembly mechanism among the diazotrophs of the salinity-driven stratified waters of Kongsfjorden. The principal environmental and ecological drivers of the observed variations were identified. The majority of the nifH gene sequences obtained in the present study belonged to cluster I and cluster III nifH phylotypes, accounting for 65% and 25% of the total nifH gene sequences. The nifH gene diversity and composition, irrespective of the size fractions (free-living and particle attached), showed a clear separation among water mass types, i.e., Atlantic-influenced versus glacier-influenced water mass. Higher nifH gene diversity and relative abundances of non-cyanobacterial nifH OTUs, affiliated with uncultured Rhizobiales, Burkholderiales, Alteromonadaceae, Gallionellaceae (cluster I) and uncultured Deltaproteobacteria including Desulfuromonadaceae (cluster III), were prevalent in GIW while uncultured Gammaproteobacteria and Desulfobulbaceae were abundant in AIW. The diazotrophic community assembly was dominated by stochastic processes, principally ecological drift, and to lesser degrees dispersal limitation and homogeneous dispersal. Differences in the salinity and dissolved oxygen content lead to the vertical segregation of diazotrophs among water mass types. These findings suggest that water column stratification affects the composition and assembly mechanism of diazotrophic communities and thus could affect nitrogen fixation in the Arctic fjord.

N2-fixing bacteria are more sensitive to microtopography than nitrogen addition in degraded grassland

Introduction

Soil bacteria play a crucial role in the terrestrial nitrogen (N) cycle by fixing atmospheric N2, and this process is influenced by both biotic and abiotic factors. The diversity of N2-fixing bacteria (NFB) directly reflects the efficiency of soil N fixation, and the diversity of NFB in degraded alpine meadow soil may change with different N fertilizing levels and varied slopes. However, how N addition affects the diversity of NFB in degraded alpine meadows, and whether this influence varies with slope, remain poorly understood.

Methods

We conducted an N addition field experiment at three levels (2, 5, and 10 g N·m-2·a-1) to study the effects of N addition on soil NFB diversity on two different slopes in a degraded meadow on the Tibetan Plateau.

Results

There were significant differences in the dominant bacterial species between the two slopes. The Chao1 index, species richness, and beta diversity of NFB did not differ significantly between slopes, but the Shannon index did. Interestingly, N addition had no effect on the diversity of NFB or the abundance of dominant bacteria. However, we did observe a significant change in some low-abundance NFB. The community composition and diversity of NFB were significantly positively correlated with slope and soil physicochemical properties (e.g., total potassium, pH, and total nitrogen).

Conclusions

Our study highlights the variation in NFB communities among different slopes in degraded alpine meadows and their resilience to exogenous N addition. Our results also underscore the importance of considering the effects of micro-topography on soil microbial communities in future studies of alpine ecosystems.

Bioprospecting for Isoetes cangae Endophytes with Potential to Promote Plant Growth

Isoetes cangae is a native plant found only in a permanent pond in Serra dos Carajás in the Amazon region. Plant-associated microbial communities are recognized to be responsible for biological processes essential for the health, growth, and even adaptation of plants to environmental stresses. In this sense, the aims of this work were to isolate, identify, and evaluate the properties of endophytic bacteria isolated from I. cangae. The bioprospecting of potentially growth-promoting endophytes required the following steps to be taken: isolation of endophytic colonies, molecular identification by 16S rDNA sequence analysis, and evaluation of the bacterial potential for nitrogen fixation, production of indole acetic acid and siderophores, as well as phosphate solubilization and mineralization. Bacillus sp., Rhizobium sp., Priestia sp., Acinetobacter sp., Rossellomorea sp., Herbaspirillum sp., Heyndrickxia sp., and Metabacillus sp., among other bacterial species, were identified. The isolates showed to be highly promising, evidencing the physiological importance for the plant and having the potential to promote plant growth.

Reframing the contribution of pelagic Sargassum epiphytic N2 fixation

Though nitrogen fixation by epiphytic diazotrophs on pelagic Sargassum has been recognized for decades, it has been assumed to contribute insignificantly to the overall marine nitrogen budget. This six-year study reframes this concept through long-term measurements of Sargassum community nitrogen fixation rates, and by extrapolating mass-specific rates to a theoretical square meter portion of Sargassum mat allowing for comparison of these rates to those of other marine and coastal diazotrophs. On 24 occasions from 2015 to 2021, rates of nitrogen fixation were measured using whole fronds of Sargassum collected from the western edge of the Gulf Stream off Cape Hatteras, North Carolina. Across all dates, mass-specific rates ranged from 0 to 37.77 μmol N g-1 h-1 with a mean of 4.156 μmol N g-1 h-1. Extrapolating using a mat-specific density of Sargassum, these rates scale to a range of 0 to 30,916 μmol N m-2 d-1 and a mean of 3,697 μmol N m-2 d-1. Quantifying this community's rates of nitrogen fixation over several years captured the sometimes-extreme variability in rates, characteristic of marine diazotrophs, which has not been reported in the literature to date. When these measurements are considered alongside estimates of the density of pelagic Sargassum, rates of nitrogen fixation by Sargassum's epiphytic diazotrophs rival that of their coastal macrophyte and planktonic counterparts. Given Sargassum's wide and expanding geographic range, the results of this study suggest this community may contribute reactive nitrogen on a meaningful, basin-wide scale, which merits further study.

Glacial meltwater and seasonality influence community composition of diazotrophs in Arctic coastal and open waters

The Arctic Ocean is particularly affected by climate change with unknown consequences for primary productivity. Diazotrophs-prokaryotes capable of converting atmospheric nitrogen to ammonia-have been detected in the often nitrogen-limited Arctic Ocean but distribution and community composition dynamics are largely unknown. We performed amplicon sequencing of the diazotroph marker gene nifH from glacial rivers, coastal, and open ocean regions and identified regionally distinct Arctic communities. Proteobacterial diazotrophs dominated all seasons, epi- to mesopelagic depths and rivers to open waters and, surprisingly, Cyanobacteria were only sporadically identified in coastal and freshwaters. The upstream environment of glacial rivers influenced diazotroph diversity, and in marine samples putative anaerobic sulphate-reducers showed seasonal succession with highest prevalence in summer to polar night. Betaproteobacteria (Burkholderiales, Nitrosomonadales, and Rhodocyclales) were typically found in rivers and freshwater-influenced waters, and Delta- (Desulfuromonadales, Desulfobacterales, and Desulfovibrionales) and Gammaproteobacteria in marine waters. The identified community composition dynamics, likely driven by runoff, inorganic nutrients, particulate organic carbon, and seasonality, imply diazotrophy a phenotype of ecological relevance with expected responsiveness to ongoing climate change. Our study largely expands baseline knowledge of Arctic diazotrophs-a prerequisite to understand underpinning of nitrogen fixation-and supports nitrogen fixation as a contributor of new nitrogen in the rapidly changing Arctic Ocean.

Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean

Dinitrogen (N₂) fixation is the major source of reactive nitrogen in the ocean and has been considered to occur specifically in low-latitude oligotrophic oceans. Recent studies have shown that N₂ fixation also occurs in the polar regions and thus is a global process, although the physiological and ecological characteristics of polar diazotrophs are not yet known. Here, we successfully reconstructed diazotroph genomes, including that of cyanobacterium UCYN-A (Candidatus 'Atelocyanobacterium thalassa'), from metagenome data corresponding to 111 samples isolated from the Arctic Ocean. These diazotrophs were highly abundant in the Arctic Ocean (max., 1.28% of the total microbial community), suggesting that they have important roles in the Arctic ecosystem and biogeochemical cycles. Further, we show that diazotrophs within genera Arcobacter, Psychromonas, and Oceanobacter are prevalent in the <0.2 µm fraction in the Arctic Ocean, indicating that current methods cannot capture their N₂ fixation. Diazotrophs in the Arctic Ocean were either Arctic-endemic or cosmopolitan species from their global distribution patterns. Arctic-endemic diazotrophs, including Arctic UCYN-A, were similar to low-latitude-endemic and cosmopolitan diazotrophs in genome-wide function, however, they had unique gene sets (e.g., diverse aromatics degradation genes), suggesting adaptations to Arctic-specific conditions. Cosmopolitan diazotrophs were generally non-cyanobacteria and commonly had the gene that encodes the cold-inducible RNA chaperone, which presumably makes their survival possible even in deep, cold waters of global ocean and polar surface waters. This study shows global distribution pattern of diazotrophs with their genomes and provides clues to answering the question of how diazotrophs can inhabit polar waters.

Impacts of phosphorus and nitrogen absence on microbial diversity and sulfate removal in anaerobic batch reactors

Sulfate-rich effluents have been successfully treated in anaerobic reactors using sulfate-reducing bacteria (SRB). Many authors have demonstrated that these systems require nitrogen and phosphorous supplementation to achieve high sulfate removal rates. However, the resource ratio theory assumes that some species can be dominant according to the nutritional relations used or even without external nutrient supplementation. Thus, this study evaluated the SRB communities in batch reactors without external nitrogen and phosphorus sources based on most probable number (MPN) quantification, denaturing gradient gel electrophoresis (DGGE) analyses and sequencing. The sulfate and chemical oxygen demand (COD) removal and kinetic parameters were also determined. After 100 days of operation, the sulfate and COD removal achieved 71.8 ± 10% and 86.5 ± 10%, respectively. The SRB population increased from 8.10⁶ to 4 × 10¹² MPN 100 mL^-1, and the richness of SRB bands was much higher at the end of the experiment compared to the inoculum. In addition, the sequenced bands from SRB-DGGE showed similarities to Desulfacinum infernum, Desulfobulbus sp, Syntrophobacter and Desulfomicrobium aestuarii-related sequences. Therefore, biological treatment of acid mine drainage wastewater was effective in the absence of nutrients, lowering costs and providing high sulfate removal efficiency.

Insights into the shift of microbial community related to nitrogen cycle, especially N2O in vanadium-polluted soil

Soil is a vital contributor to the production of nitrous oxide (N₂O), a potent greenhouse gas, through the nitrogen cycle, which can be influenced by accumulated vanadium (V) in soil but it is less pronounced. This work investigated the response of soil N₂O fluxes along with major nitrogen cycle products (ammonium, nitrate, and nitrite) to different vanadium contents (0, 200, 500, 800, and 1100 mg V/kg), and the underlying microbial mechanisms. N₂O fluxes was significantly influenced at high V content (1100 mg V/kg) due to its corresponding high water-soluble V content. Microbial composition and their correlations with nitrogen cycle products showed that microbes in dominant phyla (Actinobacteriota and Proteobacteria) and genus (Nocardioides, Lysobacter, Sphingomonas, and Marmoricola) might be the important contributor to N₂O fluxes regardless of the V content. Moreover, high V contents (800, and 1100 mg V/kg) could enrich microbes involved in nitrogen cycle, but weaken their correlations with nitrogen-related products, such as in genus Bacillus, and change microbial correlation with N₂O from associated with nitrate and nitrite to ammonium. Meanwhile, functional gene predication results showed that denitrifying genes nirKS and nosZ were negatively and positively correlated with V contents, respectively. These all further suggested that the shift of possible N₂O metabolic pathways induced mainly by water-soluble V might be the underlying reason for N₂O fluxes. These findings promote an understanding of the potential effect of metal pollution on N₂O fluxes in soil.

Nitrogen fixation of Cyndon dactylon: A possible strategy coping with long-term flooding in the Three Gorges Reservoir

The Three Gorges Reservoir (TGR) is one of the largest hydropower projects around the world which greatly alters the ecological function of the original ecosystem. The riparian zone of TGR is subject to a frequent fluctuation of water level, leading to severe nitrogen loss by leaching. Cyndon dactylon, a perennial stress tolerant plant, is one of the dominant plant species in the riparian zone of TGR. The underlying mechanism that C. dactylon can survive the nitrogen limitation has been under debate. In this study, we sampled the plant tissues of C. dactylon and the surrounding soils across different water levels and seasons in the riparian zone of TGR to explore the possible strategy for them to mining nitrogen. Our study found that the C. dactylon in the TGR riparian zone had endophytic nitrogen-fixing bacteria, particularly enriched in the plant foliage. The abundance of endophytic nitrogen-fixing bacteria was significantly negatively correlated with soil ammonia, nitrate, and organic matter, and significantly positively correlated with total phosphorous and moisture content. The endophytic nitrogen-fixing bacteria in C. dactylon were highly diverse, with Proteobacteria as the main dominant genera. The mutual cooperation mode among bacterial species made the endophytic nitrogen-fixing bacteria community of C. dactylon more resilient to environmental pressure, thus more readily adapting to conditions of repeated long-term flooding in the riparian zone of the TGR.

Improving the quality of barren rocky soil by culturing sweetpotato, with special reference to plant-microbes-soil interactions

Biological process is an effective strategy to improve soil quality in agroecosystems. Sweetpotato has long been cultivated in barren rocky soil (BRS) to improve soil fertility and obtain considerably high yield. However, how sweetpotato cultivation affects soil quality is still unclear. We cultured sweetpotato in virgin BRS, and investigated its transcriptome, rhizospheric microbial community and soil properties. A high sweetpotato yield (22.69 t.ha^-1) was obtained through upregulating the expression of genes associated with stress resistance, nitrogen/phosphorus/potassium (N/P/K) uptake, and root exudates transport. Meanwhile, the rhizospheric microbial diversity in BRS increased, and the rhizospheric microbial community structure became more similar to that of fertile soil, which might benefit from the increased root exudates. Notably, the relative abundances of N-fixing and P/K-solubilizing microbes increased, and the copy number of nifH increased 6.67 times. Moreover, the activities of acid, neutral, and alkaline phosphatases increased strongly from 0.63, 0.02, and 1.15-1.58, 0.31, and 2.11 mg phenol·g^-1·d^-1, respectively, and total carbon, dissolved organic carbon, available N/P content also increased, while bulk density and pH of BRS decreased, indicating the enhanced soil fertility. Our study found sweetpotato cultivation improved BRS quality through shaping microbial communities, which has important guiding significance for sustainable agriculture.

Nitrogenase resurrection and the evolution of a singular enzymatic mechanism

The planetary biosphere is powered by a suite of key metabolic innovations that emerged early in the history of life. However, it is unknown whether life has always followed the same set of strategies for performing these critical tasks. Today, microbes access atmospheric sources of bioessential nitrogen through the activities of just one family of enzymes, nitrogenases. Here, we show that the only dinitrogen reduction mechanism known to date is an ancient feature conserved from nitrogenase ancestors. We designed a paleomolecular engineering approach wherein ancestral nitrogenase genes were phylogenetically reconstructed and inserted into the genome of the diazotrophic bacterial model, Azotobacter vinelandii, enabling an integrated assessment of both in vivo functionality and purified nitrogenase biochemistry. Nitrogenase ancestors are active and robust to variable incorporation of one or more ancestral protein subunits. Further, we find that all ancestors exhibit the reversible enzymatic mechanism for dinitrogen reduction, specifically evidenced by hydrogen inhibition, which is also exhibited by extant A. vinelandii nitrogenase isozymes. Our results suggest that life may have been constrained in its sampling of protein sequence space to catalyze one of the most energetically challenging biochemical reactions in nature. The experimental framework established here is essential for probing how nitrogenase functionality has been shaped within a dynamic, cellular context to sustain a globally consequential metabolism.

Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems

BACKGROUND

Microbial communities in recirculating aquaculture systems (RAS) play a role in system success, nutrient cycling, and water quality. Considering the increasing socio-economic role of fish farming, e.g., regarding food security, an in-depth understanding of aquaculture microbial communities is also relevant from a management perspective, especially regarding the growth, development, and welfare of the farmed animal. However, the current data on the composition of microbial communities within RAS is patchy, which is partly attributable to diverging method choices that render comparative analyses challenging. Therefore, there is a need for accurate, standardized, and user-friendly methods to study microbial communities in aquaculture systems.

RESULTS

We compared sequencing approach performances (3 types of 16S short amplicon sequencing, PacBio long-read amplicon sequencing, and amplification-free shotgun metagenomics) in the characterization of microbial communities in two commercial RAS fish farms. Results showed that 16S primer choice and amplicon length affect some values (e.g., diversity measures, number of assigned taxa or distinguishing ASVs) but have no impact on spatio-temporal patterns between sample types, farms and time points. This implies that 16S rRNA approaches are adequate for community studies. The long-read amplicons underperformed regarding the quantitative resolution of spatio-temporal patterns but were suited to identify functional services, e.g., nitrification cycling and the detection of pathogens. Finally, shotgun metagenomics extended the picture to fungi, viruses, and bacteriophages, opening avenues for exploring inter-domain interactions. All sequencing datasets agreed on major prokaryotic players, such as Actinobacteriota, Bacteroidota, Nitrospirota, and Proteobacteria.

CONCLUSION

The different sequencing approaches yielded overlapping and highly complementary results, with each contributing unique data not obtainable with the other approaches. We conclude that a tiered approach constitutes a strategy for obtaining the maximum amount of information on aquaculture microbial communities and can inform basic research on community evolution dynamics. For specific and/or applied questions, single-method approaches are more practical and cost-effective and could lead to better farm management practices.

Sulfur-Ligated [2Fe-2C] Clusters as Synthetic Model Systems for Nitrogenase

Metal clusters featuring carbon and sulfur donors have coordination environments comparable to the active site of nitrogenase enzymes. Here, we report a series of di-iron clusters supported by the dianionic yldiide ligands, in which the Fe sites are bridged by two μ2-C atoms and four pendant S donors.The [L2Fe2] (L = {[Ph2P(S)]2C}2-) cluster is isolable in two oxidation levels, all-ferrous Fe2II and mixed-valence FeIIFeIII. The mixed-valence cluster displays two peaks in the Mössbauer spectra, indicating slow electron transfer between the two sites. The addition of the Lewis base 4-dimethylaminopyridine to the Fe2II cluster results in coordination with only one of the two Fe sites, even in the presence of an excess base. Conversely, the cluster reacts with 8 equiv of isocyanide tBuNC to give a monometallic complex featuring a new C-C bond between the ligand backbone and the isocyanide. The electronic structure descriptions of these complexes are further supported by X-ray absorption and resonant X-ray emission spectroscopies.

Changes in Bacterial Communities of Kumamoto Oyster Larvae During Their Early Development and Following Vibrio Infection Resulting in a Mass Mortality Event

Vibrio and Ostreid herpesvirus 1 are responsible for mass mortalities of oyster larvae in hatcheries. Relevant works have focused on their relationships with the disease when larval mortality occurs. On the contrary, little is known about how the resident microbiota in oyster larvae responds to Vibrio-infected disease causing mortality as the disease progressed, whereas this knowledge is fundamental to unveil the etiology of the disease. Here, we analyzed the temporal succession of the microbiome of Kumamoto oyster (Crassostrea sikamea) larvae during their early development, accompanied by a Vibrio-caused mortality event that occurred at the post D-stage of larval development in a shellfish hatchery in Ningbo, China, on June 2020. The main causative agent of larval mortality was attributable to Vibrio infection, which was confirmed by linearly increased Vibrio abundance over disease progression. Larval bacterial communities dramatically changed over host development and disease progression, as highlighted by reduced α-diversity and less diverse core taxa when the disease occurred. Null model and phylogenetic-based mean nearest taxon distance analyses showed that the relative importance of deterministic processes governing larval bacterial assembly initially increased over host development, whereas this dominance was depleted over disease progression. Furthermore, we screened the disease-discriminatory taxa with a significant change in their relative abundances, which could be indicative of disease progression. In addition, network analysis revealed that disease occurrence remodeled the co-occurrence patterns and niche characteristics of larval microbiota. Our findings demonstrate that the dysbiosis of resident bacterial communities and the shift of microecological mechanisms in the larval microbiome may contribute to mortality during oyster early development.

Functional significance of microbial diversity in arid soils: biological soil crusts and nitrogen fixation as a model system

Microbial communities respond to changes in environmental conditions; however, how compositional shifts affect ecosystem processes is still not well-understood and it is often assumed that different microbial communities will function equally under similar environmental conditions. We evaluated this assumption of functional redundancy using biological soil crusts (BSCs) from two arid ecosystems in Mexico with contrasting climate conditions (hot and cold deserts) following an experimental approach both in the field (reciprocal transplants) and in laboratory conditions (common garden), focusing on the community's composition and potential for nitrogen fixation. Potential of nitrogen fixation was assessed through the acetylene reduction assay. Community composition and diversity was determined with T-RFLPs of nifH gene, high throughput sequencing of 16S rRNA gene amplicons and metagenomic libraries. BSCs tended to show higher potential nitrogen fixation rates when experiencing temperatures more similar to their native environment. Moreover, changes in potential nitrogen fixation, taxonomic and functional community composition, and diversity often depended on an interactive effect of origin of the communities and the environment they experienced. We interpret our results as legacy effects that result from ecological specialization of the BSC communities to their native environment. Overall, we present evidence of nonfunctional redundancy of BSCs in terms of nitrogen fixation.

Nitrogen Fixation and Diazotrophic Community in Plastic-Eating Mealworms Tenebrio molitor L

Mealworms, the larvae of a coleopteran insect Tenebrio molitor L., are capable of eating, living on, and degrading non-hydrolyzable vinyl plastics as sole diet. However, vinyl plastics are carbon-rich but nitrogen-deficient. It remains puzzling how plastic-eating mealworms overcome the nutritional obstacle of nitrogen limitation. Here, we provide the evidence for nitrogen fixation activity within plastic-eating mealworms. Acetylene reduction assays illustrate that the nitrogen-fixing activity ranges from 12.3 ± 0.7 to 32.9 ± 9.3 nmol ethylene·h^-1·gut^-1 and the corresponding fixed nitrogen equivalents of protein are estimated as 8.6 to 23.0 µg per day per mealworm. Nature nitrogen isotopic analyses of plastic-eating mealworms provide further evidence for the assimilation of fixed nitrogen as a new nitrogen source. Eliminating the gut microbial microbiota with antibiotics impairs the mealworm's ability to fix nitrogen from the atmosphere, indicating the contribution of gut microbiota to nitrogen fixation. By using the traditional culture-dependent technique, PCR and RT-PCR of nifH gene, nitrogen-fixing bacteria diversity within the gut was detected, and the genus Klebsiella was demonstrated to be an important nitrogen-fixing symbiont. These findings first build the relationship between plastic degradation (carbon metabolism) and nitrogen fixation (nitrogen metabolism) within mealworms. Combined with previously reported plastic-degrading capability and nitrogen-fixing activity, mealworms may be potential candidates for up-recycling of plastic waste to produce protein sources.

Amino Acids in the Root Exudates of Agave lechuguilla Torr. Favor the Recruitment and Enzymatic Activity of Nutrient-Improvement Rhizobacteria

Agave lechuguilla is a widely distributed plant in arid ecosystems. It has been suggested that its microbiome is partially responsible for its great adaptability to the oligotrophic environments of the Chihuahuan Desert. To lead the recruitment of beneficial rhizobacteria, the root exudates are essential; however, the amino acids contained within these compounds had been largely overlooked. Thus, we investigated how the variations of amino acids in the rhizosphere at different growth stages of A. lechuguilla affect the rhizobacterial community composition, its functions, and activity of the beneficial bacteria. In this regard, it was found that arginine and tyrosine were related to the composition of the rhizobacterial community associated to A. lechuguilla, where the most abundant genera were from the phylum Proteobacteria and Bacteroidetes. Moreover, Firmicutes was largely represented by Bacillus in the phosphorus-mineralizing bacteria community, which may indicate its great distribution and versatility in the harsh environments of the Chihuahuan Desert. In contrast, we found a high proportion of Unknown taxa of nitrogen-fixing bacteria, reflecting the enormous diversity in the rhizosphere of these types of plants that remains to be explored. This work also reports the influence of micronutrients and the amino acids methionine and arginine over the increased activity of the nitrogen-fixing and phosphorus-mineralizing bacteria in the rhizosphere of lechuguillas. In addition, the results highlight the multiple beneficial functions present in the microbiome that could help the host to tolerate arid conditions and improve nutrient availability.

Gut microbiota contributes to lignocellulose deconstruction and nitrogen fixation of the larva of Apriona swainsoni

Apriona swainsoni is a vital forest pest prevalent in China. The larvae of A. swainsoni live solely in the branches of trees and rely entirely on the xylem for nutrition. However, there is still a lack of in-depth research on the gut microbiota's use of almost nitrogen-free wood components to provide bio-organic macromolecular components needed for their growth. Thus, in this study, the metagenome, metaproteome, and metabolome of the A. swainsoni larvae in four gut segments (foregut; midgut; anterior hindgut; posterior hindgut) were analyzed by the multi-omics combined technology, to explore the metabolic utilization mechanism of the corresponding gut microbiota of A. swainsoni. Firstly, we found that the metagenome of different gut segments was not significantly different in general, but there were different combinations of dominant bacteria and genes in different gut segments, and the metaproteome and metabolome of four gut segments were significantly different in general. Secondly, the multi-omics results showed that there were significant gradient differences in the contents of cellulose and hemicellulose in different segments of A. swainsoni, and the expression of corresponding metabolic proteins was the highest in the midgut, suggesting the metabolic characteristics of these lignocellulose components in A. swainsoni gut segments. Finally, we found that the C/N ratio of woody food was significantly lower than that of frass, and metagenomic results showed that nitrogen fixation genes mainly existed in the foregut and two hindgut segments. The expression of the key nitrogen fixing gene nifH occurred in two hindgut parts, indicating the feature of nitrogen fixation of A. swainsoni. In conclusion, our results provide direct evidence that the larvae of A. swainsoni can adapt to the relatively harsh niche conditions through the highly organized gut microbiome in four gut segments, and may play a major role in their growth.

Soil diazotrophic abundance, diversity, and community assembly mechanisms significantly differ between glacier riparian wetlands and their adjacent alpine meadows

Global warming can trigger dramatic glacier area shrinkage and change the flux of glacial runoff, leading to the expansion and subsequent retreat of riparian wetlands. This elicits the interconversion of riparian wetlands and their adjacent ecosystems (e.g., alpine meadows), probably significantly impacting ecosystem nitrogen input by changing soil diazotrophic communities. However, the soil diazotrophic community differences between glacial riparian wetlands and their adjacent ecosystems remain largely unexplored. Here, soils were collected from riparian wetlands and their adjacent alpine meadows at six locations from glacier foreland to lake mouth along a typical Tibetan glacial river in the Namtso watershed. The abundance and diversity of soil diazotrophs were determined by real-time PCR and amplicon sequencing based on nifH gene. The soil diazotrophic community assembly mechanisms were analyzed via iCAMP, a recently developed null model-based method. The results showed that compared with the riparian wetlands, the abundance and diversity of the diazotrophs in the alpine meadow soils significantly decreased. The soil diazotrophic community profiles also significantly differed between the riparian wetlands and alpine meadows. For example, compared with the alpine meadows, the relative abundance of chemoheterotrophic and sulfate-respiration diazotrophs was significantly higher in the riparian wetland soils. In contrast, the diazotrophs related to ureolysis, photoautotrophy, and denitrification were significantly enriched in the alpine meadow soils. The iCAMP analysis showed that the assembly of soil diazotrophic community was mainly controlled by drift and dispersal limitation. Compared with the riparian wetlands, the assembly of the alpine meadow soil diazotrophic community was more affected by dispersal limitation and homogeneous selection. These findings suggest that the conversion of riparian wetlands and alpine meadows can significantly alter soil diazotrophic community and probably the ecosystem nitrogen input mechanisms, highlighting the enormous effects of climate change on alpine ecosystems.