Search Results (58)

Single-season legume green manuring is widely promoted for soil fertility restoration in degraded agricultural lands, yet its effectiveness in alkaline semi-arid soils remains poorly understood. This study investigated the impact of first-year sweet clover (Melilotus officinalis (L.)) green manuring on soil microbiome structure and agrochemical properties in southern carbonate chernozem soils of Northern Kazakhstan. Using shotgun metagenomics, we analyzed microbial communities from sweet clover-amended soils, clean fallow, and virgin steppe reference sites. Contrary to expectations, sweet clover green manuring did not enhance soil nitrogen availability, with nitrate-N content (9.1 mg/kg) remaining lower than clean fallow (10.5 mg/kg), likely due to temporary immobilization during initial decomposition. While sweet clover significantly increased archaeal diversity (p = 0.01) and enriched nitrogen-cycling taxa, including Nitrospirae and Thaumarchaeota, overall microbial richness remained unchanged (ACE index, p > 0.05). Surprisingly, functional analysis revealed only five significant metabolic differences between sweet clover and fallow systems, indicating functional convergence of agricultural microbiomes regardless of management practice. Correlation analysis identified phosphorus as the master regulator of microbial metabolism (r = 1.0, p < 0.0001), while elevated pH (9.0), K₂O (>1000 mg/kg), and $\mathrm{N}{\mathrm{O}}_3^{-}$ showed strong negative correlations with essential metabolic pathways, revealing previously unrecognized nutrient toxicity thresholds. Virgin steppe maintained 69 unique metabolic pathways lost in agricultural systems, highlighting the ecological cost of cultivation. These findings demonstrate that sweet clover green manuring in alkaline steppe soils induces selective rather than comprehensive microbiome restructuring, with limited immediate benefits for soil fertility. This study provides critical insights for developing sustainable agricultural practices in the world’s extensive semi-arid regions facing similar edaphic constraints. Full article

Coal gangue (CG) dumped in open-air piles significantly impacts the surrounding soil environment. To investigate the effects of prolonged CG dumping on soil archaeal communities and their ecological functions, we used metagenomic sequencing to analyze soil samples, including control soil area not impacted by CG (CSL), undisturbed control sediment (CST), atmospheric dust fall area (ADF), and leachate flow area (LFA) samples. The results showed that the dominant phylum and genus of archaea were Thaumarchaeota (30.53–93.39%) and Candidatus Nitrosocosmicus (34.44–69.85%) in the different samples. Significant differences were observed in both α- and β-diversity (p < 0.05); archaeal community composition was primarily influenced by total nitrogen (TN), electrical conductivity (EC), Cu, As, and Cd. The contribution rate of As was the largest, about 44.8%. The metabolic functions of archaea were predominantly related to amino acid metabolism, and there were significant variations in carbon and nitrogen metabolic pathways in different areas. The ppdk gene showed considerable variation between ADF and CSL, and Euryarchaeota was the major contributing phylum to carbon fixation. However, for nitrogen metabolism, the gltB gene displayed marked differences, and the phylum of Thaumarchaeota was the major contributor. This study provides a theoretical foundation for land management and sustainable utilization in CG dump areas. Full article

The black soil region of Northeast China is crucial for agricultural productivity. Ammonia-oxidizing archaea (AOA) are key indicators of soil nitrification in this region, yet it remains unclear whether this process is driven by the entire community or by specific clusters. Here, we investigated the AOA community across a long-term fertilization Brown Soil Experimental Station and 15 sites in the Typical Black Soil Zone. Using Illumina MiSeq sequencing of the AOA amoA gene and cluster-specific primers, 14 OTUs were selected as core clusters based on relative abundance >0.1% and strong correlations (r > 0.7) with soil properties or PNR, and were further grouped into five distinct clusters according to phylogenetic analysis. Compared to the overall AOA community, core clusters responded more precisely to fertilization, straw addition, and spatial variation, with contrasting environmental responses reflected in their relationships with soil nitrification dynamics. Clusters G1 and G2 had positive correlations with soil PNR, while Clusters G4 and G5 had negative correlations. Moreover, AOA core clusters demonstrated stronger correlations with soil properties, including pH, C/N ratio, and NH₄⁺/NO₃⁻ ratio. These findings demonstrate that AOA core clusters are reliable microbial indicators of soil nitrification, and monitoring their abundance changes under nitrogen input can provide early insights into potential inhibition, informing predictive models and guiding more precise nitrogen management to support sustainable agricultural practices. Full article

Urban wetlands play a crucial role in maintaining ecological balance, carbon sequestration, and water purification. Sediments are key carriers for wetlands to store elements such as carbon, nitrogen, and phosphorus in the aquatic environment. This study analyzed different sediment layers of seven wetlands in Yangzhou, aiming to explore the relationship between physicochemical factors and microbial communities in wetland sediments, as well as to predict the functions of microbial communities. Functional prediction of microbial communities was conducted based on amplicon sequencing analysis, and the neutral community model was used to determine the formation and evolution process of microbial communities. The results showed that in three wetlands, namely Zhuyu Bay (ZYW), Luyang Lake (LYH), and Runyang Wetland (RYSD), the contents of carbon components (total carbon, total soluble carbon, microbial biomass carbon) in the 0–20 cm sediment layer were higher, while the carbon component contents in Baoying Lake (BYH) showed the opposite trend. Among them, the contents of total nitrogen, alkali-hydrolyzable nitrogen, total phosphorus, available phosphorus, total potassium, and available potassium in the 0–20 cm sediment layer of Runyang Wetland (RYSD) were significantly the highest. This indicates that in Runyang Wetland (RYSD), the 0–20 cm layer has more abundant carbon components and mineral nutrients compared to the 20–40 cm layer. Among the seven wetlands, it was found that the content of total potassium was all greater than 10 g/kg, which was much higher than the contents of total phosphorus and total nitrogen. Analysis of microbial communities revealed that the dominant archaeal phyla were Thaumarchaeota and Euryarchaeota, and the dominant bacterial phyla were Proteobacteria and Acidobacteria. The distribution of functional genes was mainly concentrated in Zhuyu Bay (ZYW) and Luyang Lake (LYH). Zhuyu Bay Wetland (ZYW) had potential advantages in light utilization function, and Luyang Lake (LYH) had potential advantages in carbon and nitrogen cycle functions. The assembly process of the archaeal community was mainly affected by stochastic processes, while the bacterial community was mainly affected by deterministic processes. However, water content, total phosphorus, and available potassium all had strong correlations with both archaeal and bacterial communities. The research results preliminarily reveal the connections between the physicochemical properties of sediments, microbial communities, and their potential functions in Yangzhou urban wetlands, providing an important scientific basis for the protection and management of wetland ecosystems. Full article

Seamounts are distributed globally across the oceans and are generally considered oases of biomass abundance as well as hotspots of species richness. Diverse microbial communities are essential for biogeochemical cycling, yet their functional partitioning among seamounts with geographic features remains poorly investigated. Through metagenomic sequencing and genome-resolved analysis, we revealed that Proteobacteria (33.18–40.35%) dominated the bacterial communities, while Thaumarchaeota (5.98–10.86%) were the predominant archaea. Metagenome-assembled genomes uncovered 117 medium-quality genomes, 81.91% of which lacked species-level annotation, highlighting uncultured diversity. In the Nazuna seamount, which is located in the Marcus-Wake seamount region, microbiomes exhibited heightened autotrophic potential via the 3-hydroxypropionate cycle and dissimilatory nitrate reduction, whereas in the Magellan seamounts regions, nitrification and organic nitrogen metabolism were prioritized. Sulfur oxidation genes dominated Nazuna seamount microbes, with 33 MAGs coupling denitrification to sulfur redox pathways. Metal resistance genes for tellurium, mercury, and copper were prevalent, alongside habitat-specific iron transport systems. Cross-feeding interactions mediated by manganese, reduced ferredoxin, and sulfur–metal integration suggested adaptive detoxification strategies. This study elucidates how deep-sea microbes partition metabolic roles and evolve metal resilience mechanisms across geographical niches. It also supports the view that microbial community structure and metabolic function across seamount regions are likely influenced by the geomorphological features of the seamounts. Full article

Understanding the mechanisms of protein preservation in extreme environments is essential for identifying potential molecular biosignatures on Mars. In this study, we investigated five sabkha sedimentary samples from the Abu Dhabi coast, spanning from the present day to ~11,000 years before present (BP), to assess how mineralogy and environmental conditions influence long-term protein stability. Using LC-MS/MS and direct Data-independent Acquisition (DIA) proteomic analysis, we identified 722 protein groups and 1300 peptides, revealing a strong correlation between preservation and matrix composition. Carbonate- and silica-rich samples favored the retention of DNA-binding and metal-coordinating proteins via mineral–protein interactions, while halite- and gypsum-dominated facies showed lower recovery due to extreme salinity and reduced biomass input. Functional profiling revealed a shift from metabolic dominance in modern samples to genome maintenance strategies in ancient ones, indicating microbial adaptation to prolonged environmental stress. Contrary to expectations, some ancient samples preserved large, multi-domain proteins, suggesting that early mineral encapsulation can stabilize structurally complex biomolecules over millennial timescales. Taxonomic reconstruction based on preserved proteins showed broad archaeal diversity, including Thaumarchaeota and thermophilic lineages, expanding our understanding of microbial ecology in hypersaline systems. These findings highlight sabkhas as valuable analogs for Martian evaporitic environments and suggest that carbonate–silica matrices on Mars may offer optimal conditions for preserving ancient molecular traces of life. Full article

Marine archaea play crucial roles in global biogeochemical cycles and climate regulation, yet their ecological functions in many coastal environments remain poorly understood. Jinhae Bay (JB), a eutrophic and environmentally stressed coastal system in Korea, has attracted growing attention; however, its archaeal community composition has not been characterized. In this preliminary study, we investigated the summer archaeal community structure in JB water columns based on a survey conducted in July 2018. We identified 5 archaeal phyla—primarily Euryarchaeota and Thaumarchaeota—along with 11 classes and 18 orders, with Nitrosopumilales and Methanobacteriales as dominant orders. Several ammonia-oxidizing archaea (AOA), including Candidatus Nitrosopumilus adriaticus, Candidatus Nitrosopumilus salaria, Candidatus Nitrosopumilus sediminis, and unclassified Nitrosopumilus spp., were detected. Additionally, the presence of methane-oxidizing archaea (MOA) such as Candidatus Methanoperedens nitroreducens, although at low relative abundance, suggests potential roles in nitrogen and methane cycling. These findings provide initial insights into the archaeal contributions to biogeochemical processes in JB, highlighting the need for further seasonal and functional investigations. Full article

To analyze the microbiological mechanisms of biological denitrification during low-temperature operations, continuous sampling of influent and activated sludge samples was conducted at the Changchun Municipal Wastewater Treatment Plant. The relative abundance and absolute gene abundance of ammonia-oxidizing bacteria, ammonia-oxidizing archaea, and denitrifying bacteria were determined using high-throughput sequencing technology and reverse transcription–polymerase chain reaction (RT–PCR) technology, respectively. Nitrosomonas and Nitrosospira were the dominant bacteria in ammonia-oxidizing bacteria; the detection rate was 100%; and the abundance distribution fluctuated greatly. The percentages of net proliferation rate greater than −0.05 were 75% and 62.5%, respectively, but the temperature effect was not obvious. The detection rate of Nitrosomonadaceae (norank) was 76.67%, and the percentage of net proliferation rate greater than −0.05 was 50%. The growth of ammonia-oxidizing archaea was limited at low temperature, and the abundance of most bacteria fluctuated greatly. The frequencies of net proliferation rate of Crenarchaeota (norank), Thaumarchaeota (norank), and Nitrososphaera greater than −0.05 were more than 50%. Of the 20 OUTs of denitrifying bacteria, 16 had a net increment rate greater than −0.2/d with a frequency greater than 50 per cent, of which Sinorhizobium and Alphaproteobacteria were detected with a frequency of 100% in activated sludge. The frequency of AOB and denitrifying bacteria net proliferation rate greater than zero during the low-temperature period was relatively high, which ensured the smooth progress of the denitrification process and reasonably explains the microbiological mechanism. In addition, it can be inferred that the migration of influent microorganisms can shape the population structure of denitrifying bacteria, as the net proliferation rate of most bacterial populations was less than 0. Full article

Intercropping legumes is an effective and sustainable planting pattern that has the benefit of decreasing chemical fertilizer input and improving the soil environment. However, the effects of chemical fertilizer reduction and intercropping different legumes on soil nutrients, microorganisms, and tea quality remain elusive. Hereby, compared with 100% chemical fertilizer (CK), Sesbania cannabina (SC) and Crotalaria pallida Blanco (CP) were selected as the intercropped plant with 70% chemical fertilizer to investigate its effect on soil nutrients, microorganisms, and tea quality. The results showed that compared with monocropping, intercropping legumes had greater concentrations of the soil labile organic matter, nitrate nitrogen, ammonia nitrogen, inorganic nitrogen, and alkali-hydrolyzable nitrogen. Intercropping systems significantly enhanced the content of non-ester-type catechins (catechin and gallocatechin) and ester-type catechins (epicatechin gallate). In SC, the content of gallocatechin, catechin, and epicatechin gallate increased by 146.67%, 107.69%, and 21.05%, respectively, while in CP, the content of these three compounds increased by 166.67%, 84.62%, and 19.08%, respectively. Significant differences in microbial composition were also observed under different systems. Actinobacteria, Rhodoplanes, and Thaumarchaeota were obviously enhanced in SC, while Rhodanobacter, Pseudolabrys, and Pedosphaera were manifestly improved in CP compared to those in the monoculture. Moreover, intercropping legumes significantly increased the abundances of CNP cycling functional genes, such as gpmB, mch, accD6, pgi-pmi, mcr, glmS, ACOX1 and fadB (carbohydrate metabolism), nirD and narI (nitrification), pmoB-amoB and hao (dissimilatory N reduction), and phoN (organic phosphoester hydrolysis). The relationship between intercropping systems and tea qualities was mainly established by soil nutrition and the abundance of C and N cycling functional microorganisms. This study provides more information on the relationship between soil nutrients, functional genes of microorganisms, and tea quality under tea/legume intercropping systems in tea plantations and offers a basis for the higher-performance intercropping pattern. Full article

To investigate the effects of kitchen waste on the chemical properties of acidic red soil and the community structure of ammonia–oxidizing archaea (AOA) and ammonia–oxidizing bacteria (AOB), a study was conducted in the flue–cured tobacco farmland ecosystem of the Erlongtan small watershed in central Yunnan. Eight fertilization methods were applied: no fertilization control CK, single application of chemical fertilizer T1 (1 t·hm⁻²), kitchen waste combined with a chemical fertilizer (T2:12 t·hm⁻² + 1 t·hm⁻², T3:15 t·hm⁻² + 1 t·hm⁻², T4:18 t·hm⁻² + 1 t·hm⁻²), and single application of kitchen waste (T5:12 t·hm⁻², T6:15 t·hm⁻², T7:18 t·hm⁻²). The numbers twelve, fifteen, and eighteen in brackets represent the amount of food waste applied, and one represents the amount of chemical fertilizer applied. The study evaluated the effects of kitchen waste on soil chemical properties, the community structure and composition of AOA and AOB, and the relationship between soil chemical properties and these microbial communities in acidic red soil. The results showed that: (1) single application of kitchen waste (T5, T6, T7) effectively improved soil nutrient status (SOC increased by 15.79–217.24%; TN increased by 1.53–92.99%; NH₄⁺–N increased by 18.19–520.74%; NO₃⁻–N) increased by 15.54–750.61%), and alleviated acidification. (2) Temporal variations had a more significant effect on the community structure of AOA and AOB than different treatments. The dominant phyla of AOA were Thaumarchaeota, Crenarchaeot. The dominant phylum of AOB was Proteobacteria, and the dominant genera were Nitrosospira and norank_Bacteri. (3) The number of AOA co–occurrence network nodes were equivalent to that of AOB, but AOB had more connection edges, indicating a more complex interaction network. In contrast, AOA exhibited higher modularity, reflecting tighter internal connections and greater stability. The AOA co–occurrence network showed stronger performance during the maturity and fallow stages, while AOB interactions were most active during the topping stage. (4) AOA demonstrated a strong correlation with soil chemical properties during the topping and maturity stages, whereas AOB showed a stronger correlation at the rosette and fallow stages. Among soil chemical factors, pH and SOC were identified as the primary drivers influencing AOA and AOB community abundance and structural differentiation. In conclusion, kitchen waste application enhances the nutrient content of acidic red soil and influences the niche differentiation of AOA and AOB, thereby affecting nitrogen recycling. This approach represents an environmentally friendly and sustainable fertilization method. Full article

This study aims to explore microbial activity evidence, composition of archaeal communities, and environmental constraints in coalbed-produced waters from the Hancheng Block, a representative region for coalbed methane development on the eastern margin of Ordos Basin, China. The investigation involves analyzing microbial community composition using 16S rRNA sequencing analysis as well as examining hydrogeochemical parameters. The results indicate that Euryarchaeota and Thaumarchaeota are predominant phyla within archaeal communities present in coalbed-produced water from the Hancheng Block. Among these communities, Methanobacterium is identified as the most abundant genus, followed by Methanothrix and Methanoregula. Moreover, a positive correlation is observed between the abundance of Methanobacterium and the levels of total dissolved solids as well as Mn; conversely, there is a negative correlation with dissolved organic carbon, Zn concentrations, and pH. The abundance of Co and Ni primarily influence Methanothrix while pH and Zn play significant roles in controlling Methanoregula. Additionally, No. 5 coal seam waters exhibit greater species diversity in the archaeal community compared to No. 11 counterparts. The higher abundance of archaea in the No. 5 coal seam promotes biogas generation due to the correlation between bicarbonate and dissolved inorganic carbon isotope. These research findings hold scientific significance in guiding the exploration and development of biogas within coal seams. Full article

Soil microorganisms are critical to the occurrence of Cordyceps sinensis (Chinese Cordyceps), a medicinal fungi used in Traditional Chinese Medicine. The over-collection of Chinese Cordyceps has caused vegetation degradation and impacted the sustainable occurrence of Cordyceps. The effects of Chinese Cordyceps collection on soil microorganisms have not been reported. Metagenomic analysis was performed on the soil of collecting and non-collecting areas of production and non-production areas, respectively. C. sinensis collection showed no alteration in alpha-diversity but significantly affected beta-diversity and the community composition of soil microorganisms. In Cordyceps production, Thaumarchaeota and Crenarchaeota were identified as the dominant archaeal phyla. DNA repair, flagellar assembly, propionate metabolism, and sulfur metabolism were affected in archaea, reducing the tolerance of archaea in extreme habitats. Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Nitrospirae were identified as the dominant bacterial phyla. The collection of Chinese Cordyceps enhanced the bacterial biosynthesis of secondary metabolites and suppressed ribosome and carbon metabolism pathways in bacteria. A more complex microbial community relationship network in the Chinese Cordyceps production area was found. The changes in the microbial community structure were closely related to C, N, P and enzyme activities. This study clarified soil microbial community composition and function in the Cordyceps production area and established that collection clearly affects the microbial community function by altering microbial community structure. Therefore, it would be important to balance the relationship between cordyceps production and microbiology. Full article

(1) Background: Laizhou Bay is an important aquaculture area in the north of China. Oplegnathus punctatus is one of the species with high economic benefits. In recent years, the water environment of Laizhou Bay has reached a mild eutrophication level, while microorganisms are an important group between the environment and species. In this study, we evaluated alterations in environmental elements, microbial populations, and antibiotic resistance genes (ARGs) along with their interconnections during Oplegnathus punctatus net culture. (2) Methods: A total of 142 samples from various water layers were gathered for metagenome assembly analysis. Mariculture increases the abundance of microorganisms in this culture area and makes the microbial community structure more complex. The change had more significant effects on sediment than on seawater. (3) Results: Certain populations of cyanobacteria and Candidatus Micrarchaecta in seawater, and Actinobacteria and Thaumarchaeota in sediments showed high abundance in the mariculture area. Antibiotic resistance genes in sediments were more sensitive to various environmental factors, especially oxygen solubility and salinity. (4) Conclusions: These findings highlight the complex and dynamic nature of microorganism–environment–ARG interactions, characterized by regional specificity and providing insights for a more rational use of marine resources. Full article

Studying the soils in the periodical flood zone of three reservoirs is of promising importance for their subsequent return to economic activities. Research on the bacterial and archaeal communities of soils that are periodically or continuously flooded by reservoirs is still insufficient. To evaluate the chemical status of soils and their microbiota, the study was conducted in the Yumaguzino, Nugush, and Slak reservoir sites in the South Ural area (Russian Federation). The bacterial and archaeal communities of periodically flooded and non-flooded soils were investigated after a comparative investigation of chemical, hydrological, and climatic factors. It was discovered that flooded soils had anoxic conditions during the whole of the year, with brief drying intervals of limited length and low levels of effective temperatures. In terms of chemistry, flooded soils are distinguished by increased acidity, a fall in organic matter, and an increase in alkali-hydrolysable nitrogen. Compared to their counterparts in non-flooded soils, bacterial and archaeal communities in flooded soils are significantly different. Generally speaking, the biodiversity of flooded soils rises with the duration and depth of floods. Significant variations at the phylum level are mostly caused by a decline in the relative presence of Thaumarchaeota and an increase in Proteobacteria and Chloroflexi representation. It was discovered that the Euryarchaeota phylum was either absent or had a significantly decreased relative prevalence at the sites of intermittently flooding soils. Full article

This research evaluates the development of microbiomes in primary soils, forming in various mining dumps in the arid terrain in the Republic of Bashkortostan, Russia. A metagenomic analysis of the communities was performed by sequencing extended gene sequences. The evaluation of the agro-chemical properties was in accordance with conventional pedology methods. Inverse voltammetry was used to measure the heavy metals (lead, cadmium, mercury, zinc, copper, and nickel) and arsenic content. In all the samples studied, Actinobacteria and Proteobacteria phylas dominated, and, in smaller numbers, Acidobacteria and Bacteroidetes were present. In the natural samples, the proportion of Actinobacteria was higher, and the proportions of Proteobacteria and Bacteroidetes were lower than in the samples from anthropogenically disrupted soils. Verrucomicrobia bacteria and Thaumarchaeota archaea were not found in the forming soils of the Kulyurtau and Tubinsky quarries, although in all other samples, there was a significant content of representatives of these types. Soil formation was observed at the Kulyurtau and Tubinsky mines, with a self-restoration period of more than 30 years. The microbial communities of the forming soils were similar in species richness to the background soils, and the alpha diversity showed a high level of dispersion, although the beta diversity had a different clustering, but the absence of Verrucomicrobia and Thaumarchaeota phyla in the samples from both sites indicates the underdevelopment of new soils compared with the natural background. Agrochemical indicators showed a dependence on the type of growing vegetation and the degree of anthropogenic load, and the correlation with the microbial composition of soils was traced poorly. Full article