Consumption of N2O and other N-cycle intermediates by Gemmatimonas aurantiaca strain T-27

Asymmetric succession in soil microbial communities enhances the competitive advantage of invasive alien plants

BACKGROUND

Biological invasions pose an escalating threat to native ecosystems. The accumulation of invasive alien plants worldwide is not saturated yet, underscoring the persistent and growing impact of invasions. Soil microorganisms play a key role in the process of alien plant invasion. However, the temporal dynamics of microbial communities has rarely been determined during the invasion owing to the dearth of long-term, in situ experimental systems.

RESULTS

Here, we examined the temporal succession of soil microbial communities 8 years after experiment setup in a common garden. Bacterial communities displayed divergent temporal succession, with invasive plants exhibiting higher turnover rates. Invasive alien plants reduced stochasticity in bacterial communities, likely acting as an environmental filter on community assembly. Plant growth-promoting microbes underwent higher succession rates in invasive alien plants compared to native plants, suggesting that invasive alien plants may possess a distinct advantage in fostering a favorable microbiota for their own growth and establishment. In sharp contrast, native plants selectively increased succession rates of specific plant pathogens. Furthermore, the microbial co-occurrence network was more complex in invasive plants, suggesting that invasive plants foster intricate relationships among microbial communities.

CONCLUSIONS

Therefore, the asymmetric succession in soil microbial communities enables invasive plants recruit beneficial microbiota from the surrounding soil. These results deepen our understanding of the mechanism underlying plant invasion and provide novel insights into predicting the ecological consequences resulting from widespread plant invasion. This knowledge can be incorporated into management strategies to address the evolving challenges posed by invasive plants. Video Abstract.

Seawater warming rather than acidification profoundly affects coastal geochemical cycling mediated by marine microbiome

The most concerning consequences of climate change include ocean acidification and warming, which can affect microbial communities and thus the biogeochemical cycling they mediate. Therefore, it is urgent to study the impact of ocean acidification and warming on microbial communities. In the current study, metagenomics was utilized to reveal how the structure and function of marine microorganisms respond to ocean warming and acidification. In terms of community structure, Non-metric Multidimensional Scaling analysis visualized the similarity or difference between the control and the warming or acidification treatments, but the inter-group differences were not significant. In terms of gene functionality, warming treatments showed greater effects on microbial communities than acidification. After treatment with warming, the relative abundance of genes associated with denitrification increased, suggesting that ocean nitrogen loss can increase with increased temperature. Conversely, acidification treatments apparently inhibited denitrification. Warming treatment also greatly affected sulfur-related microorganisms, increasing the relative abundance of certain sulfate-reducing prokaryote, and enriched microbial carbon-fixation pathways. These results provide information on the response strategies of coastal microorganisms in the changing marine environments.

Description of the first marine-isolated member of the under-represented phylum Gemmatimonadota, and the environmental distribution and ecogenomics of Gaopeijiales ord. nov

The phylum Gemmatimonadota is widespread but rarely cultured and, in fact, there are only six described species isolated from soil, freshwater, and wastewater treatment. However, no isolates of Gemmatimonadota from marine environment have been described; thus, little is known about the physiology and metabolism of members of the marine lineages. In this study, four novel facultatively anaerobic bacterial strains belonging to Gemmatimonadota were isolated from marine sediments collected from Xiaoshi Island in Weihai, China, using an aerobic enrichment method. The integrated results of phylogenetic and phenotypic characteristics supported that these four strains represent one novel species in a novel genus, for which the name Gaopeijia maritima gen. nov., sp. nov. is proposed, as the first representative of novel taxa, Gaopeijiales ord. nov., Gaopeijiaceae fam. nov. in the class Longimicrobiia. Gaopeijiales was detected in 22,884 out of 95,549 amplicon data sets, mainly from soil. However, the highest mean relative abundances were in sponge (0.7%) and marine sediment (0.35%), showing salt-related character. Most of the Gaopeijiales subgroups potentially belong to the rare bacterial biosphere. The aerobic enrichment in this study could significantly increase the relative abundance of Gaopeijiales (from 0.37% to 2.6%). Furthermore, the metabolic capabilities inferred from high-quality representative Gaopeijiales genomes/MAGs suggest that this group primarily performs chemoorganoheterotrophic metabolism with facultatively anaerobic characteristics and possesses various secondary metabolite biosynthesis gene clusters (BGCs), mirroring those observed in the four novel strains.IMPORTANCEDespite rapid advances in molecular and sequencing technologies, obtaining pure cultures remains a crucial research goal in microbiology, as it is essential for a deeper understanding of microbial metabolism. Gemmatimonadota is a widespread but rarely cultured bacterial phylum. Currently, there are only six cultured strains of this interesting group, all isolated from non-marine environments. Little is known about the physiology and metabolism of members of the marine lineages. Here we isolated and characterized four novel marine strains, and proposed a new order Gaopeijiales within Gemmatimonadota. Furthermore, the global distribution, environmental preference, and metabolic potential of Gaopeijiales are analyzed using public data. Our work enriches the resources available for the under-represented phylum Gemmatimonadota and provides insights into the physiological and metabolic characteristics of the marine lineage (Gaopeijiales) through culturology and omics.

Comparative Genomics Reveal Distinct Environment Preference and Functional Adaptation Among Lineages of Gemmatimonadota

Bacteria in the phylum Gemmatimonadota are globally distributed and abundant in microbial communities of various environments, playing an important role in driving biogeochemical cycling on Earth. Although high diversities in taxonomic composition and metabolic capabilities have been reported, little is known about the environmental preferences and associated functional features that facilitate adaptation among different Gemmatimonadota lineages. This study systematically analyzed the relationships between the environments, taxonomy, and functions of Gemmatimonadota lineages, by using a comparative genomics approach based on 1356 Gemmatimonadota genomes (213 high-quality and non-redundant genomes) available in a public database (NCBI). The taxonomic analysis showed that the 99.5% of the genomes belong to the class Gemmatimonadetes, and the rest of the genomes belong to the class Glassbacteria. Functional profiling revealed clear environmental preference among different lineages of Gemmatimonadota, and a marine group and two non-marine groups were identified and tested to be significantly different in functional composition. Further annotation and statistical comparison revealed a large number of functional genes (e.g., amiE, coxS, yfbK) that were significantly enriched in genomes from the marine group, supporting enhanced capabilities in energy acquisition, genetic information regulation (e.g., DNA repair), electrolyte homeostasis, and growth rate control. These genomic features are important for their survival in the marine environment, which is oligotrophic, variable, and with high salinity. The findings enhanced our understanding of the metabolic processes and environmental adaptation of Gemmatimonadota, and further advanced the understanding of the interactions of microorganisms and their habitats.

Discovery of Candidatus Nitrosomaritimum as a New Genus of Ammonia-Oxidizing Archaea Widespread in Anoxic Saltmarsh Intertidal Aquifers

Ammonia-oxidizing archaea (AOA) are widely distributed in marine and terrestrial habitats, contributing significantly to global nitrogen and carbon cycles. However, their genomic diversity, ecological niches, and metabolic potentials in the anoxic intertidal aquifers remain poorly understood. Here, we discovered and named a novel AOA genus, Candidatus Nitrosomaritimum, from the intertidal aquifers of Yancheng Wetland, showing close metagenomic abundance to the previously acknowledged dominant Nitrosopumilus AOA. Further construction of ammonia monooxygenase-based phylogeny demonstrated the widespread distribution of Nitrosomaritimum AOA in global estuarine-coastal niches and marine sediment. Niche differentiation among sublineages of this new genus in anoxic intertidal aquifers is driven by salinity and dissolved oxygen gradients. Comparative genomics revealed that Candidatus Nitrosomaritimum has the genetic capacity to utilize urea and possesses high-affinity phosphate transporter systems (phnCDE) for surviving phosphorus-limited conditions. Additionally, it contains putative nosZ genes encoding nitrous-oxide (N2O) reductase for reducing N2O to nitrogen gas. Furthermore, we gained first genomic insights into the archaeal phylum Hydrothermarchaeota populations residing in intertidal aquifers and revealed their potential hydroxylamine-detoxification mutualism with AOA through utilizing the AOA-released extracellular hydroxylamine using hydroxylamine oxidoreductase. Together, this study unravels the overlooked role of priorly unknown but abundant AOA lineages of the newly discovered genus Candidatus Nitrosomaritimum in biological nitrogen transformation and their potential for nitrogen pollution mitigation in coastal environments.

Globally distributed marine Gemmatimonadota have unique genomic potentials

BACKGROUND

Gemmatimonadota bacteria are widely distributed in nature, but their metabolic potential and ecological roles in marine environments are poorly understood.

RESULTS

Here, we obtained 495 metagenome-assembled genomes (MAGs), and associated viruses, from coastal to deep-sea sediments around the world. We used this expanded genomic catalog to compare the protein composition and update the phylogeny of these bacteria. The marine Gemmatimonadota are phylogenetically different from those previously reported from terrestrial environments. Functional analyses of these genomes revealed these marine genotypes are capable of degradation of complex organic carbon, denitrification, sulfate reduction, and oxidizing sulfide and sulfite. Interestingly, there is widespread genetic potential for secondary metabolite biosynthesis across Gemmatimonadota, which may represent an unexplored source of novel natural products. Furthermore, viruses associated with Gemmatimonadota have the potential to "hijack" and manipulate host metabolism, including the assembly of the lipopolysaccharide in their hosts.

CONCLUSIONS

This expanded genomic diversity advances our understanding of these globally distributed bacteria across a variety of ecosystems and reveals genetic distinctions between those in terrestrial and marine communities. Video Abstract.

The response of C/N/S cycling functional microbial communities to redox conditions in shallow aquifers using in-situ sediment as bio-trap matrix

Microbial communities are fundamental components driving critical biogeochemical carbon (C), nitrogen (N) and sulfur (S) cycles in groundwater ecosystems. The reduction-oxidation (redox) potential is one important environmental factor influencing the microbial community composition. Here, we developed a bio-trap method using in-situ sediment as a matrix to collect aquifer sediment samples and evaluate the response of microbial composition and C/N/S cycling functions to redox variations created by providing sole O2, joint O2 and H2, and sole H2 to three wells. Illumina sequencing analyses showed that the microbial communities in the bio-trap sediment could respond quickly to redox changes in the wells, demonstrating that this bio-trap method is promising for detecting microbial variation in the aquifer sediment. The microbial metabolic functions related to C, N and S cyclings and organic pollutants degradation were predicted by the Kyoto Encyclopedia of Genes and Genomes (KEGG) approach. It was found that the joint O2 and H2 injection produced medium oxidation-reduction potential (ORP -346 and -614 mV) and enhanced more microbial functions than sole O2 or H2, which mainly include oxidative phosphorylation, most carbon source metabolism, various pollutants degradation, and nitrogen and sulfur metabolism. Moreover, the functional genes encoding phenol monooxygenase, dioxygenase, nitrogen fixation, nitrification, aerobic and anaerobic nitrate reductase, nitrite reductase, nitric oxide reductase, and sulfur oxidation increased. These findings tell us the contaminant bioremediation and N, S metabolism can be promoted by adjusting ORP realised by injecting joint O2 and H2.

Biochar's role in improving pakchoi quality and microbial community structure in rhizosphere soil

Background

Biochar amendments enhance crop productivity and improve agricultural quality. To date, studies on the correlation between different amounts of biochar in pakchoi (Brassica campestris L.) quality and rhizosphere soil microorganisms are limited, especially in weakly alkaline soils. The experiment was set up to explore the effect of different concentrations of biochar on vegetable quality and the correlation between the index of quality and soil bacterial community structure changes.

Methods

The soil was treated in the following ways via pot culture: the blank control (CK) without biochar added and with biochar at different concentrations of 1% (T1), 3% (T2), 5% (T3), and 7% (T4). Here, we investigatedthe synergistic effect of biochar on the growth and quality of pakchoi, soil enzymatic activities, and soil nutrients. Microbial communities from pakchoi rhizosphere soil were analyzed by Illumina MiSeq.

Results

The results revealed that adding 3% biochar significantly increased plant height, root length, and dry weight of pakchoi and increased the contents of soluble sugars, soluble proteins, Vitamin C (VC), cellulose, and reduced nitrate content in pakchoi leaves. Meanwhile, soil enzyme activities and available nutrient content in rhizosphere soil increased. This study demonstrated that the the microbial community structure of bacteria in pakchoi rhizosphere soil was changed by applying more than 3% biochar. Among the relatively abundant dominant phyla, Gemmatimonadetes, Anaerolineae, Deltaproteobacteria and Verrucomicrobiae were reduced, and Alphaproteobacteria, Gammaproteobacteria, Bacteroidia, and Acidimicrobiia relative abundance increased. Furthermore, adding 3% biochar reduced the relative abundance of Gemmatimonas and increased the relative abundances of Ilumatobacter, Luteolibacter, Lysobacter, Arthrobacter, and Mesorhizobium. The nitrate content was positively correlated with the abundance of Gemmatimonadetes, and the nitrate content was significantly negatively correlated with the relative abundance of Ilumatobacter. Carbohydrate transport and metabolism in the rhizosphere soil of pakchoi decreased, and lipid transport and metabolism increased after biochar application.

Conclusion

Overall, our results indicated that applying biochar improved soil physicochemical states and plant nutrient absorption, and affected the abundance of dominant bacterial groups (e.g., Gemmatimonadetes and Ilumatobacter), these were the main factors to increase pakchoi growth and promote quality of pakchoi. Therefore, considering the growth, quality of pakchoi, and soil environment, the effect of using 3% biochar is better.

Microbial pathways of nitrous oxide emissions and mitigation approaches in drylands

Drylands refer to water scarcity and low nutrient levels, and their plant and biocrust distribution is highly diverse, making the microbial processes that shape dryland functionality particularly unique compared to other ecosystems. Drylands are constraint for sustainable agriculture and risk for food security, and expected to increase over time. Nitrous oxide (N2O), a potent greenhouse gas with ozone reduction potential, is significantly influenced by microbial communities in drylands. However, our understanding of the biological mechanisms and processes behind N2O emissions in these areas is limited, despite the fact that they highly account for total gaseous nitrogen (N) emissions on Earth. This review aims to illustrate the important biological pathways and microbial players that regulate N2O emissions in drylands, and explores how these pathways might be influenced by global changes for example N deposition, extreme weather events, and climate warming. Additionally, we propose a theoretical framework for manipulating the dryland microbial community to effectively reduce N2O emissions using evolving techniques that offer inordinate specificity and efficacy. By combining expertise from different disciplines, these exertions will facilitate the advancement of innovative and environmentally friendly microbiome-based solutions for future climate change vindication approaches.

Changes in bacterial communities induced by integrated production systems and the phenological stages of soybean

Plant development and productivity depend on interactions with soil microorganisms for nutrient availability, promotion of growth and protection against phytopathogens. Although the influence of the phenological stages of soybean crops and their environmental conditions on the soil bacterial communities have already been reported, no studies have focused on the influence of integrated agrosilvopastoral systems on bacterial consortia. In this study, we evaluated the influence of the phenological stages of soybean cultivated under conventional full sunlight (CFS) and integrated crop-livestock-forestry (ICLF) systems on bacterial communities in the rhizosphere and in bulk soil using high-throughput sequencing techniques. Proteobacteria, Actinobacteriota and Acidobacteriota were the most abundant phyla in both the rhizosphere and the bulk soil at all growth stages. The results support our hypotheses that the richness and diversity of soil bacterial communities are influenced by different cultivation systems, and that the structure of the bacterial communities in the rhizosphere and the bulk soil are modulated by the phenological stages of the soybean crop.

Natural chalcopyrite mitigates nitrous oxide emissions in sediment from coastal wetlands

Coastal wetlands are one of the most important natural sources of nitrous oxide (N2O). Previous studies have shown that copper-containing chemicals are able to reduce N2O emissions from these ecosystems. However, these chemicals may harm organisms present in coastal waters and sediment, and disturb the ecological balance of these areas. Here, we first investigated the physiological characteristics and genetic potential of denitrifying bacteria isolated from coastal wetlands. Based on an isolated denitrifier carrying a complete denitrification pathway, we tested the effect of the natural mineral chalcopyrite on N2O production by the bacteria. The results demonstrated that chalcopyrite addition lowers N2O emissions from the bacteria while increasing its N2 production rate. Among the four denitrification genes of the isolate, only nosZ gene expression was significantly upregulated following the addition of 2 mg L-1 chalcopyrite. Furthermore, chalcopyrite was applied to coastal wetland sediments. The N2O flux was significantly reduced in 50-100 mg L-1 chalcopyrite-amended sets relative to the controls. Notably, the dissolved Cu concentration in chalcopyrite-amended sediment remained within the limit set by the National Sewage Treatment Discharge Standard. qPCR and metagenomic analysis revealed that the abundance of N2O-reducing bacteria with the nosZ or nirK + nosZ genotype increased significantly in the chalcopyrite-amended groups relative to the controls, suggesting their active involvement in the reduction of N2O emissions. Our findings offer valuable insights for the use of natural chalcopyrite in large-scale field applications to reduce N2O emissions.

Microplastics affect C, N, and P cycling in natural environments: Highlighting the driver of soil hydraulic properties

As microplastics (MPs) are organic polymers with a carbon-based framework, they may affect nutrient cycling. Information regarding how MPs influence N, P, and C cycling and the underlying driving force remains lacking. N, P, and C cycling induced by soil hydraulic properties under MPs exposure (including polyethylene (PE), polyvinyl chloride (PVC), polystyrene (PS), polypropylene (PP)) in the natural environment were investigated in this study. MPs exposure increased the soil water content (11.2-84.5%) and reduced bulk density (11.4-42.8%); soil saturated hydraulic conductivity increased by 7.3-69.4% under PP and PE exposure. MPs exposure led to increases in available phosphorus, NO3--N, NH4+-N, and soil organic matter; the bacterial communities related to N and C cycling were significantly changed. Expression levels of soil N and C cycling-related genes were enhanced under low concentrations (0.5% and 2%) of MPs, except PVC; consequently, soil nitrogen storage and organic carbon storage increased by 12-75% and 6.7-93%, respectively. Correlation analyses among soil hydraulic properties, bacterial communities, and functional genes related to nutrient cycling revealed that soil hydraulic properties (including soil water content, saturated water capacity, and soil saturated hydraulic conductivity) were the dominant factors affecting soil N and C storage under MPs exposure.

Multi-environment ecogenomics analysis of the cosmopolitan phylum Gemmatimonadota

Gemmatimonadota is a diverse bacterial phylum commonly found in environments such as soils, rhizospheres, fresh waters, and sediments. So far, the phylum contains just six cultured species (five of them sequenced), which limits our understanding of their diversity and metabolism. Therefore, we analyzed over 400 metagenome-assembled genomes (MAGs) and 5 culture-derived genomes representing Gemmatimonadota from various aquatic environments, hydrothermal vents, sediments, soils, and host-associated (with marine sponges and coral) species. The principal coordinate analysis based on the presence/absence of genes in Gemmatimonadota genomes and phylogenomic analysis documented that marine and host-associated Gemmatimonadota were the most distant from freshwater and wastewater species. A smaller genome size and coding sequences (CDS) number reduction were observed in marine MAGs, pointing to an oligotrophic environmental adaptation. Several metabolic pathways are restricted to specific environments. For example, genes for anoxygenic phototrophy were found only in freshwater, wastewater, and soda lake sediment genomes. There were several genomes from soda lake sediments and wastewater containing type IC/ID ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Various genomes from wastewater harbored bacterial type II RuBisCO, whereas RuBisCO-like protein was found in genomes from fresh waters, soil, host-associated, and marine sediments. Gemmatimonadota does not contain nitrogen fixation genes; however, the nosZ gene, involved in the reduction of N2O, was present in genomes from most environments, missing only in marine water and host-associated Gemmatimonadota. The presented data suggest that Gemmatimonadota evolved as an organotrophic species relying on aerobic respiration and then remodeled its genome inventory when adapting to particular environments. IMPORTANCE Gemmatimonadota is a rarely studied bacterial phylum consisting of a handful of cultured species. Recent culture-independent studies documented that these organisms are distributed in many environments, including soil, marine, fresh, and waste waters. However, due to the lack of cultured species, information about their metabolic potential and environmental role is scarce. Therefore, we collected Gemmatimonadota metagenome-assembled genomes (MAGs) from different habitats and performed a systematic analysis of their genomic characteristics and metabolic potential. Our results show how Gemmatimonadota have adapted their genomes to different environments.

Hyperarid soil microbial community response to simulated rainfall

The exceptionally long and protracted aridity in the Atacama Desert (AD), Chile, provides an extreme, terrestrial ecosystem that is ideal for studying microbial community dynamics under hyperarid conditions. Our aim was to characterize the temporal response of hyperarid soil AD microbial communities to ex situ simulated rainfall (5% g water/g dry soil for 4 weeks) without nutrient amendment. We conducted replicated microcosm experiments with surface soils from two previously well-characterized AD hyperarid locations near Yungay at 1242 and 1609 masl (YUN1242 and YUN1609) with distinct microbial community compositions and average soil relative humidity levels of 21 and 17%, respectively. The bacterial and archaeal response to soil wetting was evaluated by 16S rRNA gene qPCR, and amplicon sequencing. Initial YUN1242 bacterial and archaeal 16S rRNA gene copy numbers were significantly higher than for YUN1609. Over the next 4 weeks, qPCR results showed significant increases in viable bacterial abundance, whereas archaeal abundance decreased. Both communities were dominated by 10 prokaryotic phyla (Actinobacteriota, Proteobacteria, Chloroflexota, Gemmatimonadota, Firmicutes, Bacteroidota, Planctomycetota, Nitrospirota, Cyanobacteriota, and Crenarchaeota) but there were significant site differences in the relative abundances of Gemmatimonadota and Chloroflexota, and specific actinobacterial orders. The response to simulated rainfall was distinct for the two communities. The actinobacterial taxa in the YUN1242 community showed rapid changes while the same taxa in the YUN1609 community remained relatively stable until day 30. Analysis of inferred function of the YUN1242 microbiome response implied an increase in the relative abundance of known spore-forming taxa with the capacity for mixotrophy at the expense of more oligotrophic taxa, whereas the YUN1609 community retained a stable profile of oligotrophic, facultative chemolithoautotrophic and mixotrophic taxa. These results indicate that bacterial communities in extreme hyperarid soils have the capacity for growth in response to simulated rainfall; however, historic variations in long-term hyperaridity exposure produce communities with distinct putative metabolic capacities.

Distribution, abundance, and ecogenomics of the Palauibacterales, a new cosmopolitan thiamine-producing order within the Gemmatimonadota phylum

The phylum Gemmatimonadota comprises mainly uncultured microorganisms that inhabit different environments such as soils, freshwater lakes, marine sediments, sponges, or corals. Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or metagenome-assembled genome (MAG) has been characterized. Here, we carried out a broad study of the distribution, abundance, ecotaxonomy, and metabolism of PAUC43f, for which we propose the name of Palauibacterales. This group was detected in 4,965 16S rRNA gene amplicon datasets, mainly from marine sediments, sponges, corals, soils, and lakes, reaching up to 34.3% relative abundance, which highlights its cosmopolitan character, mainly salt-related. The potential metabolic capabilities inferred from 52 Palauibacterales MAGs recovered from marine sediments, sponges, and saline soils suggested a facultative aerobic and chemoorganotrophic metabolism, although some members may also oxidize hydrogen. Some Palauibacterales species might also play an environmental role as N2O consumers as well as suppliers of serine and thiamine. When compared to the rest of the Gemmatimonadota phylum, the biosynthesis of thiamine was one of the key features of the Palauibacterales. Finally, we show that polysaccharide utilization loci (PUL) are widely distributed within the Gemmatimonadota so that they are not restricted to Bacteroidetes, as previously thought. Our results expand the knowledge about this cryptic phylum and provide new insights into the ecological roles of the Gemmatimonadota in the environment. IMPORTANCE Despite advances in molecular and sequencing techniques, there is still a plethora of unknown microorganisms with a relevant ecological role. In the last years, the mostly uncultured Gemmatimonadota phylum is attracting scientific interest because of its widespread distribution and abundance, but very little is known about its ecological role in the marine ecosystem. Here we analyze the global distribution and potential metabolism of the marine Gemmatimonadota group PAUC43f, for which we propose the name of Palauibacterales order. This group presents a saline-related character and a chemoorganoheterotrophic and facultatively aerobic metabolism, although some species might oxidize H2. Given that Palauibacterales is potentially able to synthesize thiamine, whose auxotrophy is the second most common in the marine environment, we propose Palauibacterales as a key thiamine supplier to the marine communities. This finding suggests that Gemmatimonadota could have a more relevant role in the marine environment than previously thought.

Long-term fertilization coupled with rhizobium inoculation promotes soybean yield and alters soil bacterial community composition

Microbial diversity is an important indicator of soil fertility and plays an indispensable role in farmland ecosystem sustainability. The short-term effects of fertilization and rhizobium inoculation on soil microbial diversity and community structure have been explored extensively; however, few studies have evaluated their long-term effects. Here, we applied quantitative polymerase chain reaction (qPCR) and amplicon sequencing to characterize the effect of 10-year fertilizer and rhizobium inoculation on bacterial communities in soybean bulk and rhizosphere soils at the flowering-podding and maturity stages. Four treatments were examined: non-fertilization control (CK), phosphorus and potassium fertilization (PK), nitrogen and PK fertilization (PK + N), and PK fertilization and Bradyrhizobium japonicum 5821 (PK + R). Long-term co-application of rhizobium and PK promoted soybean nodule dry weight by 33.94% compared with PK + N, and increased soybean yield by average of 32.25%, 5.90%, and 5.00% compared with CK, PK, and PK + N, respectively. The pH of PK + R was significantly higher than that of PK and PK + N at the flowering-podding stage. The bacterial abundance at the flowering-podding stage was positively correlated with soybean yield, but not at the maturity stage. The significant different class Gemmatimonadetes, and the genera Gemmatimonas, and Ellin6067 in soil at the flowering-podding stage were negatively correlated with soybean yield. However, the bacterial community at class and genus levels at maturity had no significant effect on soybean yield. The key bacterial communities that determine soybean yield were concentrated in the flowering-podding stage, not at maturity stage. Rhizosphere effect, growth period, and treatment synergies resulted in significant differences in soil bacterial community composition. Soil organic matter (OM), total nitrogen (TN), pH, and available phosphorus (AP) were the main variables affecting bacterial community structure. Overall, long-term co-application of rhizobium and fertilizer not only increased soybean yield, but also altered soil bacterial community structure through niche reconstruction and microbial interaction. Rhizobium inoculation plays key role in reducing nitrogen fertilizer application and promoting sustainable agriculture practices.

Lower Compositional Variation and Higher Network Complexity of Rhizosphere Bacterial Community in Constructed Wetland Compared to Natural Wetland

Macrophyte rhizosphere microbes, as crucial components of the wetland ecosystem, play an important role in maintaining the function and stability of natural and constructed wetlands. Distinct environmental conditions and management practices between natural and constructed wetlands would affect macrophytes rhizosphere microbial communities and their associated functions. Nevertheless, the understanding of the diversity, composition, and co-occurrence patterns of the rhizosphere bacterial communities in natural and constructed wetlands remains unclear. Here, we used 16S rRNA gene high-throughput sequencing to characterize the bacterial community of the rhizosphere and bulk sediments of macrophyte Phragmites australis in representative natural and constructed wetlands. We observed higher alpha diversity of the bacterial community in the constructed wetland than that of the natural wetland. Additionally, the similarity of bacterial community composition between rhizosphere and bulk sediments in the constructed wetland was increased compared to that of the natural wetland. We also found that plants recruit specific taxa with adaptive functions in the rhizosphere of different wetland types. Rhizosphere samples of the natural wetland significantly enriched the functional bacterial groups that mainly related to nutrient cycling and plant-growth-promoting, while those of the constructed wetland-enriched bacterial taxa with potentials for biodegradation. Co-occurrence network analysis showed that the interactions among rhizosphere bacterial taxa in the constructed wetland were more complex than those of the natural wetland. This study broadens our understanding of the distinct selection processes of the macrophytes rhizosphere-associated microbes and the co-occurrence network patterns in different wetland types. Furthermore, our findings emphasize the importance of plant-microbe interactions in wetlands and further suggest P. australis rhizosphere enriched diverse functional bacteria that might enhance the wetland performance through biodegradation, nutrient cycling, and supporting plant growth.

Clarifying Microbial Nitrous Oxide Reduction under Aerobic Conditions: Tolerant, Intolerant, and Sensitive

One of the major challenges for the bioremediation application of microbial nitrous oxide (N2O) reduction is its oxygen sensitivity. While a few strains were reported capable of reducing N2O under aerobic conditions, the N2O reduction kinetics of phylogenetically diverse N2O reducers are not well understood. Here, we analyzed and compared the kinetics of clade I and clade II N2O-reducing bacteria in the presence or absence of oxygen (O2) by using a whole-cell assay with N2O and O2 microsensors. Among the seven strains tested, N2O reduction of Stutzerimonas stutzeri TR2 and ZoBell was not inhibited by oxygen (i.e., oxygen tolerant). Paracoccus denitrificans, Azospirillum brasilense, and Gemmatimonas aurantiaca reduced N2O in the presence of O2 but slower than in the absence of O2 (i.e., oxygen sensitive). N2O reduction of Pseudomonas aeruginosa and Dechloromonas aromatica did not occur when O2 was present (i.e., oxygen intolerant). Amino acid sequences and predicted structures of NosZ were highly similar among these strains, whereas oxygen-tolerant N2O reducers had higher oxygen consumption rates. The results suggest that the mechanism of O2 tolerance is not directly related to NosZ structure but is rather related to the scavenging of O2 in the cells and/or accessory proteins encoded by the nos cluster. IMPORTANCE Some bacteria can reduce N2O in the presence of O2, whereas others cannot. It is unclear whether this trait of aerobic N2O reduction is related to the phylogeny and structure of N2O reductase. The understanding of aerobic N2O reduction is critical for guiding emission control, due to the common concurrence of N2O and O2 in natural and engineered systems. This study provided the N2O reduction kinetics of various bacteria under aerobic and anaerobic conditions and classified the bacteria into oxygen-tolerant, -sensitive, and -intolerant N2O reducers. Oxygen-tolerant N2O reducers rapidly consumed O2, which could help maintain the low O2 concentration in the cells and keep their N2O reductase active. These findings are important and useful when selecting N2O reducers for bioremediation applications.

Nitrate determines the bacterial habitat specialization and impacts microbial functions in a subsurface karst cave

Karst caves are usually considered as natural laboratories to study pristine microbiomes in subsurface biosphere. However, effects of the increasingly detected nitrate in underground karst ecosystem due to the acid rain impact on microbiota and their functions in subsurface karst caves have remained largely unknown. In this study, samples of weathered rocks and sediments were collected from the Chang Cave, Hubei province and subjected to high-throughput sequencing of 16S rRNA genes. The results showed that nitrate significantly impacted bacterial compositions, interactions, and functions in different habitats. Bacterial communities clustered according to their habitats with distinguished indicator groups identified for each individual habitat. Nitrate shaped the overall bacterial communities across two habitats with a contribution of 27.2%, whereas the pH and TOC, respectively, structured bacterial communities in weathered rocks and sediments. Alpha and beta diversities of bacterial communities increased with nitrate concentration in both habitats, with nitrate directly affecting alpha diversity in sediments, but indirectly on weathered rocks by lowering pH. Nitrate impacted more on bacterial communities in weathered rocks at the genus level than in sediments because more genera significantly correlated with nitrate concentration in weathered rocks. Diverse keystone taxa involved in nitrogen cycling were identified in the co-occurrence networks such as nitrate reducers, ammonium-oxidizers, and N2-fixers. Tax4Fun2 analysis further confirmed the dominance of genes involved in nitrogen cycling. Genes of methane metabolism and carbon fixation were also dominant. The dominance of dissimilatory and assimilatory nitrate reduction in nitrogen cycling substantiated nitrate impact on bacterial functions. Our results for the first time revealed the impact of nitrate on subsurface karst ecosystem in terms of bacterial compositions, interactions, and functions, providing an important reference for further deciphering the disturbance of human activities on the subsurface biosphere.

New insights into the effects of chlorpyrifos on soil microbes: Carbon and nitrogen cycle related microbes in wheat/maize rotation agricultural field

Chlorpyrifos, a broad-spectrum organophosphorus insecticide, has been widely detected worldwide and is a potential neurotoxin and endocrine disruptor. Besides, chlorpyrifos has been proven that have a negative effect on soil microbes. In the present study, chlorpyrifos formulation (LORSBAN®, 45% emulsifiable concentrate) was applied in an agricultural field at the recommended dose (R dose, 270.0 and 337.5 g a.i. ha^-1 for wheat and maize respectively) and double recommended (DR) dose. Chlorpyrifos residue level and effect on soil microbes related to soil carbon and nitrogen cycle function were analyzed. Results showed that the half-lives of chlorpyrifos in wheat and maize field soil were 7.23-8.23 and 1.45-1.77 d, respectively. Application of chlorpyrifos at even DR dose did not result in unacceptable residual chlorpyrifos, where the final residual chlorpyrifos in wheat/maize (leaf, stem, and grain) was meet the requirement of the maximum residual limit (0.5 mg kg^-1 for wheat and 0.05 mg kg^-1 for maize) in China. Chlorpyrifos enhanced the activity of β-glucosidase by increasing the relative abundance of Sphingosinicella and promoted the carbon cycle in wheat field. The changes of cbbLR and cbbLG gene abundance also confirmed that chlorpyrifos could affect the import and export of soil carbon pool. The effect of chlorpyrifos on soil N cycle was determined by changes in the abundance of the bacterial genus Gemmatimonas, which is associated with denitrification. Further analysis of N-cycle functional genes and urease activity showed that chlorpyrifos inhibited nitrogen fixation in wheat field, but promoted nitrogen fixation in maize field. In general, bacterial abundance, urease, and AOA-amoA gene could be early warning markers of chlorpyrifos contamination. The results demonstrated the negative effects of chlorpyrifos on soil microbes especially on soil C and N cycle in actual agricultural field. It provides new insights about chlorpyrifos environmental pollution and its effect on soil ecosystems.

Soybean continuous cropping affects yield by changing soil chemical properties and microbial community richness

In agroecosystems, different cropping patterns cause changes in soil physicochemical properties and thus in microbial communities, which in turn affect crop yields. In this study, the yields of soybean continuous cropping for 5 years (C5), 10 years (C10), and 20 years (C20) and of soybean-corn rotational cropping (R) treatments were determined, and samples of the tillage layer soil were collected. High-throughput sequencing technology was used to analyze the diversity and composition of the soil bacterial and fungal communities. The factors influencing microbial communities, along with the effects of these communities and those of soil chemical indexes on yield, were further evaluated. The results showed that the community richness index of bacteria was higher in C20 than in R and that of fungi was highest in C5. The differences in the bacterial and fungal communities diversity indexes were not significant among the different continuous cropping treatments, respectively. The soil microbial community composition of all continuous cropping treatments differed significantly from R. The dominant bacterial phylum was Actinobacteriota and the dominant fungal phylum was Ascomycota. The relative abundance of Fusarium did not differ significantly among the continuous cropping treatments, while that of the plant pathogen fungi Lectera sp., Plectosphaerella sp., and Volutella sp. increased with continuous cropping years. Soil pH, SOM, N, and TP had significant effects on both bacterial and fungal communities, and TK and C/N had highly significant effects on fungal communities. The yield of C5 was significantly lower than that of R, and the differences in yield between C10, C20, and R were not significant. TN, TP, and pH had significant effects on yield, and fungal community abundance had a greater negative effect on yield than bacterial community abundance.

Addition of carbon sources and nutrient salts can inhibit gangue acidification by changing microbial community structure

Acidic pollution from gangue oxidation has become a primary environmental problem in coal mining areas in China. The use of microorganisms to remediate acidic pollution in coal gangue piles has been indicated to be effective, but environmental differences and carbon sources in different mining areas have become important factors restricting microbial activity. Instead of the addition of new functional bacteria to gangue piles, carbon sources and nutrient salts were added to recently discharged gangue to enhance the activity of beneficial bacteria in the indigenous microbial community. The changes in pH and electrical conductivity (EC) of the gangue leachate as well as the composition and abundance of the functional microbial community on the surface of the gangue were analyzed by leaching simulation experiments and 16S rRNA sequencing. The results showed that the addition of a carbon source maintained the pH of the gangue leachate at 6.31~6.65 in 14 d, which was significantly higher than that of the control group, but the pH of the leachate decreased significantly after the addition of the carbon source was stopped. The most effective treatment is adding a low concentration of nutrient salt (20% concentration) and sodium lactate (0.02 g/L) to the gangue first, and then adding sodium lactate (0.1 mg/L) every 7 days. The addition of carbon sources and nutrient salts changed the microbial community composition on the surface of the gangue, and the species diversity index decreased. The dominant genera in the experimental group were Listeria, Arthrobacter, and Enterococcus. The functional gene types in the experimental and control groups were almost the same, but their relative abundance changed. The abundance of functional genes related to the sulfur cycle increased substantially in the experimental group, and the abundance of genes involved in the nitrogen and carbon cycles also increased, albeit to different degrees.

Consumption of N2O by Flavobacterium azooxidireducens sp. nov. Isolated from Decomposing Leaf Litter of Phragmites australis (Cav.)

Microorganisms acting as sinks for the greenhouse gas nitrous oxide (N₂O) are gaining increasing attention in the development of strategies to control N₂O emissions. Non-denitrifying N₂O reducers are of particular interest because they can provide a real sink without contributing to N₂O release. The bacterial strain under investigation (IGB 4-14^T), isolated in a mesocosm experiment to study the litter decomposition of Phragmites australis (Cav.), is such an organism. It carries only a nos gene cluster with the sec-dependent Clade II nosZ and is able to consume significant amounts of N₂O under anoxic conditions. However, consumption activity is considerably affected by the O₂ level. The reduction of N₂O was not associated with cell growth, suggesting that no energy is conserved by anaerobic respiration. Therefore, the N₂O consumption of strain IGB 4-14^T rather serves as an electron sink for metabolism to sustain viability during transient anoxia and/or to detoxify high N₂O concentrations. Phylogenetic analysis of 16S rRNA gene similarity revealed that the strain belongs to the genus Flavobacterium. It shares a high similarity in the nos gene cluster composition and the amino acid similarity of the nosZ gene with various type strains of the genus. However, phylogenomic analysis and comparison of overall genome relatedness indices clearly demonstrated a novel species status of strain IGB 4-14^T, with Flavobacterium lacus being the most closely related species. Various phenotypic differences supported a demarcation from this species. Based on these results, we proposed a novel species Flavobacterium azooxidireducens sp. nov. (type strain IGB 4-14^T = LMG 29709^T = DSM 103580^T).

Effects of Two Kinds of Commercial Organic Fertilizers on Growth and Rhizosphere Soil Properties of Corn on New Reclamation Land

Due to the development of urbanization and industrialization, a large amount of cultivated land resources has been occupied, while new reclamation land could expand the supply of usable land for food security. Organic fertilizers, such as crop residues, biosolids, sheep manure, mushroom residue, and biogas liquid, have been considered as an effective amendment in immature soil to improve its quality. Recently, two kinds of commercial organic fertilizers, pig manure and mushroom residue organic fertilizer (PMMR-OF), and sheep manure organic fertilizer (SM-OF), have been more regularly applied in agriculture production. However, the information available on effect of the two kinds of fertilizers on plant growth and rhizosphere soil properties in immature field is very limited. In order to evaluate PMMR-OF and SM-OF on immature soil, the soil quality and microbial community structure of corn rhizosphere soil samples under the two kinds of organic fertilizers at different concentrations was investigated. The results revealed a significant difference between commercial organic fertilizers (especially SM-OF) and chemical compound fertilizers (CCF) in soil properties and microbial community structure. Indeed, compared with the control based on16S and ITS amplicon sequencing of soil microflora, SM-OF caused a 10.79-19.52%, 4.33-4.39%,and 14.58-29.29% increase in Proteobacteria, Actinobacteria, and Ascomycota, but a 5.82-20.58%, 0.53-24.06%, 10.87-16.79%, 2.69-10.50%, 44.90-59.24%, 8.88-10.98%, and 2.31-21.98% reduction in Acidobacteria, Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Basidiomycota, Mortierellomycota, and Chytridiomycota, respectively. CCF caused a 24.11%, 23.28%, 38.87%, 19.88%, 18.28%, and 13.89% reduction in Acidobacteria, Gemmatimonadetes, Bacteroidetes, Verrucomicrobia, Basidiomycota, Chytridiomycota, but a 22.77%, 41.28%, 7.88%, and 19.39% increase in Proteobacteria, Actinobacteria, Ascomycota, and Mortierellomycota, respectively. Furthermore, redundancy discriminant analysis of microbial communities and soil properties of PMMR-OF, SM-OF, CCF, and the control treatments indicated that the main variables of bacterial and fungal communities included organic matter content, available P, and available K. Overall, the results of this study revealed significant changes under different fertilizer conditions (PMMR-OF, SM-OF, CCF, under different concentrations) in microbiota and chemical properties of corn soil. Commercial organic fertilizers, particularly SM-OF, can be used as a good amendment for the new reclamation land.

A potential network structure of symbiotic bacteria involved in carbon and nitrogen metabolism of wood-utilizing insect larvae

Effective biological utilization of wood biomass is necessary worldwide. Since several insect larvae can use wood biomass as a nutrient source, studies on their digestive microbial structures are expected to reveal a novel rule underlying wood biomass processing. Here, structural inferences for inhabitant bacteria involved in carbon and nitrogen metabolism for beetle larvae, an insect model, were performed to explore the potential rules. Bacterial analysis of larval feces showed enrichment of the phyla Chroloflexi, Gemmatimonadetes, and Planctomycetes, and the genera Bradyrhizobium, Chonella, Corallococcus, Gemmata, Hyphomicrobium, Lutibacterium, Paenibacillus, and Rhodoplanes, as bacteria potential involved in plant growth promotion, nitrogen cycle modulation, and/or environmental protection. The fecal abundances of these bacteria were not necessarily positively correlated with their abundances in the habitat, indicating that they were selectively enriched in the feces of the larvae. Correlation and association analyses predicted that common fecal bacteria might affect carbon and nitrogen metabolism. Based on these hypotheses, structural equation modeling (SEM) statistically estimated that inhabitant bacterial groups involved in carbon and nitrogen metabolism were composed of the phylum Gemmatimonadetes and Planctomycetes, and the genera Bradyrhizobium, Corallococcus, Gemmata, and Paenibacillus, which were among the fecal-enriched bacteria. Nevertheless, the selected common bacteria, i.e., the phyla Acidobacteria, Armatimonadetes, and Bacteroidetes and the genera Candidatus Solibacter, Devosia, Fimbriimonas, Gemmatimonas Opitutus, Sphingobium, and Methanobacterium, were necessary to obtain good fit indices in the SEM. In addition, the composition of the bacterial groups differed depending upon metabolic targets, carbon and nitrogen, and their stable isotopes, δ¹³C and δ¹⁵N, respectively. Thus, the statistically derived causal structural models highlighted that the larval fecal-enriched bacteria and common symbiotic bacteria might selectively play a role in wood biomass carbon and nitrogen metabolism. This information could confer a new perspective that helps us use wood biomass more efficiently and might stimulate innovation in environmental industries in the future.

(Meta)Genomic Analysis Reveals Diverse Energy Conservation Strategies Employed by Globally Distributed Gemmatimonadota

Gemmatimonadota is a phylum-level lineage distributed widely but rarely reported. Only six representatives of Gemmatimonadota have so far been isolated and cultured in laboratory. The physiology, ecology, and evolutionary history of this phylum remain unknown. The 16S rRNA gene survey of our salt lake and deep-sea sediments, and Earth Microbiome Project (EMP) samples, reveals that Gemmatimonadota exist in diverse environments globally. In this study, we retrieved 17 metagenome-assembled genomes (MAGs) from salt lake sediments (12 MAGs) and deep-sea sediments (5 MAGs). Analysis of these MAGs and the nonredundant MAGs or genomes from public databases reveals Gemmatimonadota can degrade various complex organic substrates, and mainly employ heterotrophic pathways (e.g., glycolysis and tricarboxylic acid [TCA] cycle) for growth via aerobic respiration. And the processes of sufficient energy being stored in glucose through gluconeogenesis, followed by the synthesis of more complex compounds, are prevalent in Gemmatimonadota. A highly expandable pangenome for Gemmatimonadota has been observed, which presumably results from their adaptation to thriving in diverse environments. The enrichment of the Na⁺/H⁺ antiporter in the SG8-23 order represents their adaptation to salty habitats. Notably, we identified a novel lineage of the SG8-23 order, which is potentially anoxygenic phototrophic. This lineage is not closely related to the phototrophs in the order of Gemmatimonadales. The two orders differ distinctly in the gene organization and phylogenetic relationship of their photosynthesis gene clusters, indicating photosystems in Gemmatimonadota have evolved in two independent routes.

IMPORTANCE The phylum Gemmatimonadota is widely distributed in various environments. However, their physiology, ecology and evolutionary history remain unknown, primary due to the limited cultured isolates and available genomes. We were intrigued to find out how widespread this phylum is, and how it can thrive under diverse conditions. Our results here expand the knowledge of the genetic and metabolic diversity of Gemmatimonadota, and shed light on the diverse energy conservation strategies (i.e., oxidative phosphorylation, substrate phosphorylation, and photosynthetic phosphorylation) responsible for their global distribution. Moreover, gene organization and phylogenetic analysis of photosynthesis gene clusters in Gemmatimonadota provide a valuable insight into the evolutionary history of photosynthesis.

Effects of Different Microbial Fertilizers on Growth and Rhizosphere Soil Properties of Corn in Newly Reclaimed Land

Land reclamation may expand the supply of usable land for food security. Soil microorganisms have been considered as an amendment in immature soil to improve its quality. However, different microbial fertilizers' effects on plant growth in immature soil have largely been unexplored. In order to evaluate the effects of different microbial fertilizers on immature soil, the soil quality and microbial community structure of corn rhizosphere soil samples under different microbial fertilizers were investigated. The results revealed a significant difference between microbial fertilizers (especially seaweed microbial fertilizer, SMF) and commercial chemical compound fertilizers in the soil properties and microbial community structure. Indeed, SMF caused a 486.21%, 23.17%, 21.08%, 38.33%, and 482.39% increase in Flavobacteriaceae, Planctomycetaceae, Chitinophagaceae, Acidobacteria_Gp3, and Mortierellaceae but a 23.82%, 18.66%, 42.36%, 29.12%, 81.97%, 42.19%, and 99.33% reduction in Cytophagales, Comamonadaceae, Rhodospirillaceae, Sinobacteaceae, Aspergillaceae, Myrmecridiaceae, and Typhulaceae, respectively; while CCF caused an 85.68% and 183.22% increase in Xanthomonadaceae and Mortierellaceae but a 31.29%, 36.02%, and 65.74% reduction in Cytophagales, Spartobacteria, and Cyphellophoraceae compared with the control based on 16S and ITS amplicon sequencing of soil microflora. Furthermore, redundancy discriminant analysis of the microbial communities and soil properties indicated that the main variables of the bacterial and fungal communities included exchangeable Ca, organic matter content, total N, and available P. Overall, the results of this study revealed significant changes under different fertilizer conditions in the microbiota and chemical properties of corn soil. Microbial fertilizers, particularly SMF and SM, can be used as a good amendment for newly reclaimed land.

Effects of microplastics and carbon nanotubes on soil geochemical properties and bacterial communities

A 100-day soil incubation experiment was conducted to explore the effects of conventional (high-density polyethylene, HDPE) and biodegradable (polylactic acid, PLA) microplastics (MPs) and multiwall carbon nanotubes (MWCNTs) on soil geochemical properties and bacterial communities. Generally, soil pH was increased by 10% HDPE and 10% PLA, but decreased by increasing MWCNTs. Soil dissolved organic carbon content was only increased by 10% PLA. NO₃^--N content was significantly decreased by MPs, with a decrement of 99% by 10% PLA. Similarly, available P content was reduced by 10% MPs. The activities of urease and alkaline phosphatase were stimulated by 10% PLA, but generally inhibited by HDPE. Conversely, FDAse activity was stimulated by HDPE, but inhibited by 10% PLA, whereas invertase activity decreased with increasing MWCNTs. Overall, both MPs and MWCNTs changed soil bacterial diversity. Co-exposure to 10% MPs and MWCNTs of 1 and 10 mg/kg caused the lowest species richness and Shannon indexes. MPs especially at the 10% dose changed bacterial community composition and the associated metabolic pathways, causing the enrichment of specific taxa and functional genes. Our findings show that conventional and biodegradable MPs differently change soil geochemical properties and microbial community structure and functions, which can be further modified by co-existing MWCNTs.

Microbial communities in swamps of four mangrove reserves driven by interactions between physicochemical properties and microbe in the North Beibu Gulf, China

Mangroves are distributed in coastal and estuarine regions and are characterized as a sink for terrestrial pollution. It is believed that complex interactions between environmental factors and microbial communities exist in mangrove swamps. However, little is known about environment-microbe interactions. There is a need to clarify some important environmental factors shaping microbial communities and how environmental factors interact with microbial assemblages in mangrove swamps. In the present study, physicochemical and microbial characteristics in four mangrove reserves (named ZZW, Qin, Bei, and GQ) in the North Beibu Gulf were determined. The interactions between environmental factors and microbial assemblages were analyzed with statistical methods in addition to CCA and RDA. Higher concentrations of sulfate (SO₄^2--S) and Fe but lower concentrations of total phosphorus (TP) and NO₃^--N were detected in ZZW and Qin. Nutrient elements (NO₃^--N, NH₄⁺-N, organic matter (OM), SO₄^2--S, Fe, and TP) were more important than heavy metals for determining the microbial assemblages, and NO₃^--N was the most important factor. NO₃^--N, SO₄^2--S, TP, and Fe formed a significant co-occurrence network in conjunction with some bacterial taxa, most of which were Proteobacteria. Notably, comparatively elevated amounts of sulfate-reducing bacteria (Desulfatibacillum, Desulfomonile, and Desulfatiglans) and sulfur-oxidizing bacteria (Thioprofundum and Thiohalophilus) were found in ZZW and Qin. The co-occurrence network suggested that some bacteria involved in sulfate reduction and sulfur oxidation drive the transformation of P and N, resulting in the reduction of P and N in mangrove swamps. Through the additional utilization of multivariate regression tree (MRT) and co-occurrence network analysis, our research provides a new perspective for understanding the interactions between environmental factors and microbial communities in mangroves.

N2O Reduction by Gemmatimonas aurantiaca and Potential Involvement of Gemmatimonadetes Bacteria in N2O Reduction in Agricultural Soils

Agricultural soil is the primary N₂O sink limiting the emission of N₂O gas into the atmosphere. Although Gemmatimonadetes bacteria are abundant in agricultural soils, limited information is currently available on N₂O reduction by Gemmatimonadetes bacteria. Therefore, the effects of pH and temperature on N₂O reduction activities and affinity constants for N₂O reduction were examined by performing batch experiments using an isolate of Gemmatimonadetes bacteria, Gemmatimonas aurantiaca (NBRC100505^T). G. aurantiaca reduced N₂O at pH 5–9 and 4–50°C, with the highest activity being observed at pH 7 and 30°C. The affinity constant of G. aurantiaca cells for N₂O was 4.4‍ ‍μM. The abundance and diversity of the Gemmatimonadetes 16S rRNA gene and nosZ encoding nitrous oxide reductase in agricultural soil samples were also investigated by quantitative PCR (qPCR) and amplicon sequencing ana­lyses. Four N₂O-reducing agricultural soil samples were assessed, and the copy numbers of the Gemmatimonadetes 16S rRNA gene (clades G1 and G3), nosZ DNA, and nosZ mRNA were 8.62–9.65×10⁸, 5.35–7.15×10⁸, and 2.23–4.31×10⁹ copies (g dry soil)^–1, respectively. The abundance of the nosZ mRNA of Gemmatimonadetes bacteria and OTU91, OUT332, and OTU122 correlated with the N₂O reduction rates of the soil samples tested, suggesting N₂O reduction by Gemmatimonadetes bacteria. Gemmatimonadetes 16S rRNA gene reads affiliated with OTU4572 and OTU3759 were predominant among the soil samples examined, and these Gemmatimonadetes OTUs have been identified in various types of soil samples.

Long-Term Persistence of Arbuscular Mycorrhizal Fungi in the Rhizosphere and Bulk Soils of Non-host Brassica napus and Their Networks of Co-occurring Microbes

Arbuscular mycorrhizal fungi (AMF) are obligate plant symbionts that improve the nutrition and health of their host. Most, but not all the crops form a symbiosis with AMF. It is the case for canola (Brassica napus), an important crop in the Canadian Prairies that is known to not form this association. From 2008 to 2018, an experiment was replicated at three locations of the Canadian Prairies and it was used to assess the impact of canola on the community of AMF naturally occurring in three cropping systems, canola monoculture, or canola in two different rotation systems (2-years, canola-wheat and 3-years, barley-pea-canola). We sampled canola rhizosphere and bulk soils to: (i) determine diversity and community structure of AMF, we expected that canola will negatively impact AMF communities in function of its frequency in crop rotations and (ii) wanted to assess how these AMF communities interact with other fungi and bacteria. We detected 49 AMF amplicon sequence variants (ASVs) in canola rhizosphere and bulk soils, confirming the persistence of a diversified AMF community in canola-planted soil, even after 10 years of canola monoculture, which was unexpected considering that canola is among non-mycorrhizal plants. Network analysis revealed a broad range of potential interactions between canola-associated AMF and some fungal and bacterial taxa. We report for the first time that two AMF, Funneliformis mosseae and Rhizophagus iranicus, shared their bacterial cohort almost entirely in bulk soil. Our results suggest the existence of non-species-specific AMF-bacteria or AMF-fungi relationships that could benefit AMF in absence of host plants. The persistence of an AMF community in canola rhizosphere and bulk soils brings a new light on AMF ecology and leads to new perspectives for further studies about AMF and soil microbes interactions and AMF subsistence without mycotrophic host plants.

Phylum Gemmatimonadota and Its Role in the Environment

Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.

Effects of excessive nitrogen on nitrogen uptake and transformation in the wetland soils of Liaohe estuary, northeast China

It remains unclear whether excessive nitrogen additions lead to the degradation of Suaeda salsa (S. salsa) by affecting the nitrogen pool, enzyme activities, and bacterial community structure of wetland soils. This study investigated the effect of five added nitrogen concentrations (0, 1, 2, 4, and 6 mmol L^-1 N with NH₄NO₃ = group C, group L, group M, group H, and group G, respectively) on nitrogen uptake by S. salsa and nitrogen transformation in the wetland soils of the Liaohe estuary. The height, weight, and total nitrogen (TN) of S. salsa in group G was significantly lower than in the other groups (p <0.05). The NH₄⁺-N concentration in the soil tended to increase with increasing nitrogen addition, but the TN concentration in the soil tended to decrease. The nitrogenase, protease, urease, ammonia monooxygenase (AMO), nitrous oxide reductase (NOR), and dehydrogenase (DHA) activities increased with increasing nitrogen addition within the range of 0 to 4 mmol L^-1. We identified 30 phyla and 48 known genera across all five groups. The predominant phyla were Proteobacteria (52.68%), Bacteroidetes (22.58%), and Planctomycetes (3.94%). The most abundant genus was Acinetobacter (13.38%), followed by Proteiniphilum (11.88%) and Brevundimonas (6.03%). The total number of soil bacterial species increased with increasing nitrogen addition. Group G had lower soil bacterial activity and diversity than the other groups. It was concluded that appropriate levels of nitrogen addition could promote nitrogen uptake by S. salsa and nitrogen transformation in the wetland soils of the Liaohe estuary by affecting soil enzyme activities and soil bacterial activity, diversity, abundance, and composition, while excessive nitrogen additions may be one of the reasons for the degradation of S. salsa.

Soil characteristics and microbial community response in rare earth mining areas in southern Jiangxi Province, China

The microbial community and functional flora in rare earth mining areas are correlated, but the characteristics and metabolic pathways of pollutant in such mining areas are still poorly known. The heavy metals, rare earth elements, and microorganisms present after mining of rare earth mine sites were analyzed. After mining, all sampling sites exhibited low pH and low total organic carbon levels, accompanied by high iron and aluminum concentrations. The development of vegetation is closely related to the development of microorganisms. In the complex environment of rare earth mining areas, Proteobacteria exhibit an absolute competitive advantage. During mine environmental recovery, the relative abundances of Acidobacteria and Chloroflexi will increase markedly, and with further restoration the relative abundance of Firmicutes will gradually decrease. Many genera of bacteria related to the N cycle and heavy metal metabolism were detected in the study area, indicating the important metabolic pathways for ammonia nitrogen and heavy metals in rare earth mining areas. Bacterial genera that promote plant nitrogen fixation also occur in the area, further revealing the nitrogen cycle. This research is important for health assessment and recovery of rare earth mines.

Destruction of the soil microbial ecological environment caused by the over-utilization of the rice-crayfish co-cropping pattern

The rice-crayfish co-cropping pattern is a traditional method for the intensive utilization of rice fields. In recent years, this pattern has been over-developed in many countries and regions, especially in China, because of its simple agronomic technology and high economic benefits. However, little is known about the potential ecological problems regarding soil microorganisms caused by the over-utilization of this pattern. The results show that rice-crayfish co-cropping, when over-utilized for a long time, reduced soil microbial richness and diversity compared with rice monocropping. A decrease in bacterial abundance in the nitrogen cycle and an increase in bacterial abundance in the carbon cycle led to a decrease in the nitrogen cycle function and an increase in the carbon cycle function. In an analysis of bacteria that are sensitive to cropping patterns, it was found that in the rice-crayfish co-cropping, the relative abundances of sensitive OTUs from Firmicutes (Bacillus and Clostridium) and Chloroflexi (Anaerolineaceae) were significantly higher during the entire growth period than those observed in the rice monocropping pattern, while the relative abundances of sensitive OTUs from Nitrospirae (Nitrospira), Gemmatimonadetes (Gemmatimonas), and Actinobacteria (Nocardioides) were significantly lower than those observed in the rice monocropping pattern. A network analysis shows that growth-period-sensitive OTUs drive the co-occurrence network modules, although the OTUs also have positive and negative correlations among modules but a positive synergistic effect on the regulation of soil nutrients. In addition, OTUs that were sensitive at the booting stage and filling stage were the key microbial groups in the rice-crayfish co-cropping and rice monocropping networks, respectively. Understanding the classifications and functions of sensitive microbes present during the rice growth period is the basis for formulating a microbial flora management strategy for the rice-crayfish co-cropping pattern, which is of great significance for adjusting agricultural management measures and controlling current soil microbial ecological problems.

Beyond denitrification: The role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions

Many biotic and abiotic processes contribute to nitrous oxide (N₂ O) production in the biosphere, but N₂ O consumption in the environment has heretofore been attributed primarily to canonical denitrifying microorganisms. The nosZ genes encoding the N₂ O reductase enzyme, NosZ, responsible for N₂ O reduction to dinitrogen are now known to include two distinct groups: the well-studied Clade I which denitrifiers typically possess, and the novel Clade II possessed by diverse groups of microorganisms, most of which are non-denitrifiers. Clade II N₂ O reducers could play an important, previously unrecognized role in controlling N₂ O emissions for several reasons, including: (1) the consumption of N₂ O produced by processes other than denitrification, (2) hypothesized non-respiratory functions of NosZ as an electron sink or for N₂ O detoxification, (3) possible differing enzyme kinetics of Clade II NosZ compared to Clade I NosZ, and (4) greater nosZ gene abundance for Clade II compared to Clade I in soils of many ecosystems. Despite the potential ecological significance of Clade II NosZ, a census of 800 peer-reviewed original research articles discussing nosZ and published from 2013 to 2019 showed that the percentage of articles evaluating or mentioning Clade II nosZ increased from 5% in 2013 to only 22% in 2019. The census revealed that the slowly spreading awareness of Clade II nosZ may result in part from disciplinary silos, with the percentage of nosZ articles mentioning Clade II nosZ ranging from 0% in Agriculture and Agronomy journals to 32% in Multidisciplinary Sciences journals. In addition, inconsistent nomenclature for Clade I nosZ and Clade II nosZ, with 17 different terminologies used in the literature, may have created confusion about the two distinct groups of N₂ O reducers. We provide recommendations to accelerate advances in understanding the role of the diversity of N₂ O reducers in regulating soil N₂ O emissions.

Comparing the long-term responses of soil microbial structures and diversities to polyethylene microplastics in different aggregate fractions

Microplastics (MPs) alter soil aggregation stability. However, studies have yet to determine whether these alterations further affect microbial community structures and diversities within different soil aggregates and whether they influence the responses of soil microbial structures and diversities to MPs in different aggregate fractions. In this study, long-term soil incubation experiments and soil fractionation were combined to investigate the effects of polyethylene microplastics (PE-MPs) on soil aggregate properties and microbial communities in soil aggregates with different particle sizes. Results showed that the existence of PE-MPs significantly reduced the physicochemical properties of soil aggregates, inhibited the activities of soil enzymes, and changed the richness and diversity of bacterial and fungal communities. Such variations exerted notable differences in soil aggregate levels. The response sensitivity of bacteria in the silt and clay fraction was higher than that in the macroaggregate fraction, but the response sensitivity of fungi in the macroaggregate fraction was higher than that in the silt and clay fraction. Relationships and path analysis between soil aggregate properties and microbial communities after PE-MPs addition were proposed. PE-MPs affected microbial community structures by directly and indirectly influencing soil microenvironmental conditions. The relative abundances of Acidobacteria, Gemmatimonadetes, Bacteroides, Basidiomycota, Chtridiomyota, and Glomeromycota were significantly correlated with physicochemical properties and soil enzyme activities. Enzyme activities were direct factors influencing soil microbial community structures, and physicochemical properties (i.e., dissolved organic carbon, soil available phosphorus) could indirectly affect these structures by acting on soil enzyme activities. Our findings helped improve our understanding of the responses of soil microbial structures and diversities to MPs through the perspective of different soil aggregates.

Defining the wheat microbiome: Towards microbiome-facilitated crop production

Wheat is one of the world's most important crops, but its production relies heavily on agrochemical inputs which can be harmful to the environment when used excessively. It is well known that a multitude of microbes interact with eukaryotic organisms, including plants, and the sum of microbes and their functions associated with a given host is termed the microbiome. Plant-microbe interactions can be beneficial, neutral or harmful to the host plant. Over the last decade, with the development of next generation DNA sequencing technology, our understanding of the plant microbiome structure has dramatically increased. Considering that defining the wheat microbiome is key to leverage crop production in a sustainable way, here we describe how different factors drive microbiome assembly in wheat, including crop management, edaphic-environmental conditions and host selection. In addition, we highlight the benefits to take a multidisciplinary approach to define and explore the wheat core microbiome to generate solutions based on microbial (synthetic) communities or single inoculants. Advances in plant microbiome research will facilitate the development of microbial strategies to guarantee a sustainable intensification of crop production.

Gemmatimonas groenlandica sp. nov. Is an Aerobic Anoxygenic Phototroph in the Phylum Gemmatimonadetes

The bacterial phylum Gemmatimonadetes contains members capable of performing bacteriochlorophyll-based phototrophy (chlorophototrophy). However, only one strain of chlorophototrophic Gemmatimonadetes bacteria (CGB) has been isolated to date, hampering our further understanding of their photoheterotrophic lifestyle and the evolution of phototrophy in CGB. By combining a culturomics strategy with a rapid screening technique for chlorophototrophs, we report the isolation of a new member of CGB, Gemmatimonas (G.) groenlandica sp. nov., from the surface water of a stream in the Zackenberg Valley in High Arctic Greenland. Distinct from the microaerophilic G. phototrophica strain AP64^T, G. groenlandica strain TET16^T is a strictly aerobic anoxygenic phototroph, lacking many oxygen-independent enzymes while possessing an expanded arsenal for coping with oxidative stresses. Its pigment composition and infra-red absorption properties are also different from G. phototrophica, indicating that it possesses a different photosystem apparatus. The complete genome sequence of G. groenlandica reveals unique and conserved features in the photosynthesis gene clusters of CGB. We further analyzed metagenome-assembled genomes of CGB obtained from soil and glacier metagenomes from Northeast Greenland, revealing a wide distribution pattern of CGB beyond the stream water investigated.

Application of a microbial consortium improves the growth of Camellia sinensis and influences the indigenous rhizosphere bacterial communities

AIMS

To investigate the role of a microbial consortium in influencing of Camellia sinensis growth and rhizosphere bacteria microbial community structure.

METHODS AND RESULTS

Based on glasshouse trials, the microbial consortium TCM was selected for a field trial. TCM significantly increased bud density (67·53%), leaf area (31·15%) and hundred-bud weight (22·5%) compared with the control treatment (P < 0·01) during 180 days. Furthermore, TCM-treated soil showed a significant increase (P < 0·05) in organic matter (60·89%), total nitrogen (66·22%), total phosphorus (3·34%), available phosphorus (3·82%), available potassium (9·24%) and 2-3 mm water-stable aggregates (77·93%). Molecular ecological network analysis of the rhizobacteria indicated an increase in modularity and the number of community, connection and nodes after TCM application. Several plant growth-promoting bacteria were categorized as hubs or indicators, such as Haliangium, Catenulispora and Gemmatimonas, and showed intensive connections with other bacteria.

CONCLUSIONS

The TCM consortium enhances the effectiveness of soil mineral nutrition, influences the indigenous rhizobacterial community, alters the rhizobacterial network structure in the rhizosphere and promotes the growth of C. sinensis.

SIGNIFICANCE AND IMPACT OF THE STUDY

The TCM growth-promoting mechanism was closely related to rhizosphere bacterial diversity; therefore, strengthening rhizobacterial interactions may help promote C. sinensis growth, which could be a sustainable approach for improving C. sinensis growth and health in tea plantations.

BALOs Improved Gut Microbiota Health in Postlarval Shrimp (Litopenaeus vannamei) After Being Subjected to Salinity Reduction Treatment

White shrimp, Litopenaeus vannamei, is a widely farmed species. In China, shrimp postlarvae (PL) are frequently subjected to salinity reduction treatment to meet end growers' needs. However, although this treatment effectively reduces vibrio counts, its impact on gut microbiota health is still unknown. In this study, we applied a euryhaline strain of BALOs, BDN-1F2 (BD), and Bacillus subtilis (SD) to the rearing of second-generation shrimp PL after salinity reduction treatment so as to determine if they could impact PL gut microbiota by using high-throughput sequencing analysis. Results show that PL gut microbiota, both compositionally and functionally, have been badly wrecked after salinity reduction treatment with the generally recognized as opportunistic pathogens Gammaproteobacteria being the only dominant class at day 1 of test, viz., 99.43, 85.61, and 83.28% in BD, SD, and control (CD) groups, respectively. At day 7, Gammaproteobacteria was still the only dominant class in the SD and CD groups with relative abundance of 99.77 and 99.87% correspondingly, whereas in the BD group, its value dropped to 8.44%. Regarding biodiversity parameter the Shannon index, over the 7-day test period, while the SD group was unchanged (0.98-0.93), the CD group dropped to 0.94 from 2.94, and the BD group was raised to 7.14 from 0.93. Functionally, compared to control, the SD group displayed similar strength of various predicted community functions, but the BD group had hugely enhanced its various capabilities (p < 0.05). These results demonstrated that the addition of BDN-1F2 had exceedingly improved PL gut microbiota health by raising its biodiversities and strengthening its functionalities. On reviewing data derived from this as well as relevant studies, a Shannon index cutoff value was tentatively suggested so as to differentiate microbiota-healthy PL7-15 from the unhealthy ones. Furthermore, a conceptual mechanism of BALOs in the rectification/improvement of the microbial community health has also been proposed.

Hierarchical detection of diverse Clade II (atypical) nosZ genes using new primer sets for classical- and multiplex PCR array applications

The reduction of nitrous oxide (N₂O) to N₂ represents the key terminal step in canonical denitrification. Nitrous oxide reductase (NosZ), the enzyme associated with this biological step, however, is not always affiliated with denitrifying microorganisms. Such organisms were shown recently to possess a Clade II (atypical) nosZ gene, in contrast to Clade I (typical) nosZ harbored in more commonly studied denitrifiers. Subsequent phylogenetic analyses have shown that Clade II NosZ are affiliated with a much broader diversity of microorganisms than those with Clade I NosZ, the former including both non-denitrifiers and denitrifiers. Most studies attempting to characterize the nosZ gene diversity using DNA-based PCR approaches have only focused on Clade I nosZ, despite recent metagenomic sequencing studies that have demonstrated the dominance of Clade II nosZ genes in many ecosystems, particularly soil. As a result, these studies have greatly underestimated the genetic potential for N₂O reduction present in ecosystems. Because the high diversity of Clade II NosZ makes it impossible to design a universal primer set that would effectively amplify all nosZ genes in this clade, we developed a suite of primer sets to specifically target seven of ten designated subclades of Clade II nosZ genes. The new primer sets yield suitable product sizes for paired end amplicon sequencing and qPCR, demonstrated here in their use for both conventional single-reaction and multiplex array platforms. In addition, we show the utility of these primers for detecting nosZ gene transcripts from mRNA extracted from soil.