Search Results (19)

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

The Okinawa Trough (OT) has been a focus of scientific research for many years due to the presence of vibrant hydrothermal and cold seep activity within its narrow basin. However, the spatial distribution and environmental drivers of microbial communities in OT sediments remain poorly understood. The present study aims to address this knowledge gap by investigating microbial diversity and abundance at ten different sampling sites in a transitional zone between hydrothermal vents and cold seeps in the OT. The microbial community at two sampling sites (G08 and G09) in close proximity to hydrothermal vents showed a high degree of similarity. However, lower bacterial and archaeal abundances were found in these sites. The archaeal groups, classified as Hydrothermarchaeota and Thermoplasmata, showed a comparatively higher relative abundance at these sites. In addition, ammonia-oxidizing archaea (AOA), from the family Nitrosopumilaceae, were found to have a higher relative abundance in the OT surface sediments at sampling sites G03, G04, G05, G06, and G07. This result suggests that ammonia oxidation may be actively occurring in these areas. Furthermore, Methylomirabilaceae, which are responsible for methane oxidation coupled with nitrite reduction, dominated three sampling sites (G07, G08, and G09), implying that N-DAMO may play an important role in mitigating methane emissions. Using the FAPROTAX database, we found that predicted prokaryotic microbial functional groups involved in methyl-reducing methanogenesis and hydrogenotrophic methanogenesis were most abundant at sites G08 and G09. At sampling sites G01 and G02, functional groups such as hydrocarbon degradation, methanotrophy, methanol oxidation, denitrification, sulfate respiration, and sulfur oxidation were more abundant. Nitrogen content is the most important environmental factor determining the bacterial and archaeal communities in the OT surface sediments. These results expand our knowledge of the spatial distribution of microbial communities in the transitional zone between hydrothermal vents and cold seeps in the OT. Full article

Certain plant species have developed the ability to express biological nitrification inhibition (BNI), suppressing the activity of nitrifying microbes and thereby reducing the conversion of ammonium to nitrate. This study assessed the BNI capacity and the rhizosphere ammonia-oxidizing microbiome of two grass species: the endemic Australian Barley Mitchell grass (Astrebla pectinata) and the introduced koronivia grass (Urochloa humidicola), using soils from both agricultural land and native vegetation. In agricultural soil, koronivia grass exhibited significantly higher BNI capacity compared with Barley Mitchell grass. However, in native soil, this trend was reversed, with Barley Mitchell grass demonstrating a significantly greater BNI capacity than koronivia grass (52% vs. 38%). Koronivia grass significantly altered the composition of the ammonia-oxidizing bacteria community in its rhizosphere, leading to a decrease in the Shannon index and bacteria number. Conversely, Barley Mitchell grass reduced the Shannon index (1.2 vs. 1.7) and population size (3.28 × 10⁷ vs. 7.43 × 10⁷ gene copy number g⁻¹ dry soil) of the ammonia-oxidizing archaea community in its rhizosphere to a greater extent. These findings suggest that Australian Barley Mitchell grass may have evolved mechanisms to suppress soil archaeal nitrifiers, thereby enhancing its BNI capacity and adapting to Australia’s nutrient-poor soils. Full article

The Kuril–Kamchatka Trench (North-West Pacific Ocean) is included in the deepest trenches (>9000 m). This study is the first that aims at uncovering the bathyal prokaryotic diversity (1000–2000 m) of this fascinating extreme environment. The analysis of α-diversity revealed that bacterial communities showed greater diversity than archaeal communities and that both communities were characterized by poor evenness (indicative of the presence of few dominant OTUs). The metabarcoding analysis showed that Proteobacteria (65.5–90.7%), Bacteroidetes (2.4–10.7%), and Actinobacteria (2.5–9.6%) were the highly represented phyla of bacteria, with Acinetobacter (21.5–62.5%) as the most abundant genus. Moreover, the recently described Pseudofrancisella genus, which has been isolated from estuarine environments, has been found among the major bacterial taxa. This work represents the first report stating the presence of this genus in bathyal waters. The archaeal communities were dominated by the phylum Thaumarchaeota (53.6–94.0%), with Nitrosopumilus (53.6–94%) as its representative genus. The functional diversity analysis revealed that overall, the bacterial communities had a higher involvement in the carbon and nitrogen biogeochemical cycles, with chemoheterotrophy (mostly aerobic), aromatic compound degradation, and nitrate reduction as the most represented functions. In the archaeal communities, the most represented ecological function was the aerobic oxidation of ammonia (first stage of nitrification), a functional feature characteristic of Nitrosopumilus. Full article

We analyzed the amplicons of the 16S rRNA genes and assembled metagenome-assembled genomes (MAGs) of the enrichment culture from the Fe-Mn layer to have an insight into the diversity and metabolic potential of microbial communities from sediments of two sites in the northern basin of Lake Baikal. Organotrophic Chloroflexota, Actionobacteriota, and Acidobacteriota, as well as aerobic and anaerobic participants of the methane cycle (Methylococcales and Methylomirabilota, respectively), dominated the communities of the surface layers. With depth, one of the cores showed a decrease in the proportion of the Chloroflexota and Acidobacteriota members and a substantial increase in the sequences of the phylum Firmicutes. The proportion of the Desulfobacteriota and Thermodesulfovibronia (Nitrospirota) increased in another core. The composition of archaeal communities was similar between the investigated sites and differed in depth. Members of ammonia-oxidizing archaea (Nitrososphaeria) predominated in the surface sediments, with an increase in anaerobic methanotrophs (Methanoperedenaceae) and organoheterotrophs (Bathyarchaeia) in deep sediments. Among the 37 MAGs, Gammaproteobacteria, Desulfobacteriota, and Methylomirabilota were the most common in the microbial community. Metagenome sequencing revealed the assembled genomes genes for N, S, and CH₄ metabolism for carbon fixation, and genes encoding Fe and Mn pathways, indicating the likely coexistence of the biogeochemical cycle of various elements and creating certain conditions for the development of taxonomically and functionally diverse microbial communities. Full article

Beside natural factors, human activities are important for the development of microbiomes. Thus, local soil bacterial communities are affected by recent activities such as agriculture, mining and industry. In addition, ancient human impacts dating back centuries or millennia have changed soils and can emboss the recent bacterial communities up to now, representing a certain long-term “memory of soil”. Soil samples from five different archaeological excavation places were investigated for the presence of Archaea with a Next Generation Sequencing (NGS) analysis of the DNA coding for 16S r-RNA sequences. It was found that the abundance of Archaea differs strongly between less than one and more than 40 percent of bacteria. A Principal Component Analysis (PCA) of all samples shows that the archaeological excavation places can be distinguished from each other by the archaeal component of soil bacterial communities, which presents a typical pattern for each place. Most samples are marked by the dominance of Crenarchaeota, which are presented mainly by ammonia-related types. High contents of Nanoarchaeaota have been observed in one ash deposit of a historical saline and all samples of a historical tannery area. These samples are also marked by a significant presence of Dadabacteria. The specific abundancies of special Archaea—among them ammonia-oxidizing and sulphur-related types—are due obviously to former human activities and support the concept of the “ecological memory of soil”. Full article

The Arctic is warming 2–3 times faster than the global average, leading to a decrease in Arctic sea ice extent, thickness, and associated changes in sea ice structure. These changes impact sea ice habitat properties and the ice-associated ecosystems. Sea-ice algal blooms provide various algal-derived carbon sources for the bacterial and archaeal communities within the sea ice. Here, we detail the transition of these communities from winter through spring to early summer during the Norwegian young sea ICE (N-ICE2015) expedition. The winter community was dominated by the archaeon Candidatus Nitrosopumilus and bacteria belonging to the Gammaproteobacteria (Colwellia, Kangiellaceae, and Nitrinocolaceae), indicating that nitrogen-based metabolisms, particularly ammonia oxidation to nitrite by Cand. Nitrosopumilus was prevalent. At the onset of the vernal sea-ice algae bloom, the community shifted to the dominance of Gammaproteobacteria (Kangiellaceae, Nitrinocolaceae) and Bacteroidia (Polaribacter), while Cand. Nitrosopumilus almost disappeared. The bioinformatically predicted carbohydrate-active enzymes increased during spring and summer, indicating that sea-ice algae-derived carbon sources are a strong driver of bacterial and archaeal community succession in Arctic sea ice during the change of seasons. This implies a succession from a nitrogen metabolism-based winter community to an algal-derived carbon metabolism-based spring/ summer community. Full article

The metagenomic whole genome shotgun sequencing (mWGS) approach was used to detect signatures of the rhizosphere microbiomes of Dipterygium glaucum and surrounding bulk soil microbiomes, and to detect differential microbial responses due to watering. Preliminary results reflect the reliability of the experiment and the rationality of grouping microbiomes. Based on the abundance of non-redundant genes, bacterial genomes showed the highest level, followed by Archaeal and Eukaryotic genomes, then, the least abundant viruses. Overall results indicate that most members of bacteria have a higher abundance/relative abundance (AB/RA) pattern in the rhizosphere towards plant growth promotion, while members of eukaryota have a higher pattern in bulk soil, most likely acting as pathogens. The results also indicate the contribution of mycorrhiza (genus Rhizophagus) in mediating complex mutualistic associations between soil microbes (either beneficial or harmful) and plant roots. Some of these symbiotic relationships involve microbes of different domains responding differentially to plant root exudates. Among these are included the bacterial genus Burkholderia and eukaryotic genus Trichoderma, which have antagonistic activities against the eukaryotic genus Fusarium. Another example involves Ochrobactrum phage POA1180, its bacterial host and plant roots. One of the major challenges in plant nutrition involves other microbes that manipulate nitrogen levels in the soil. Among these are the microbes that perform contraversal actions of nitrogen fixation (the methanogen Euryarchaeota) and ammonia oxidation (Crenarchaeota). The net nitrogen level in the soil is originally based on the AB/RA of these microbes and partially on the environmental condition. Watering seems to influence the AB/RA of a large number of soil microbes, where drought-sensitive microbes (members of phyla Acidobacteria and Gemmatimonadetes) showed an increased AB/RA pattern after watering, while others (Burkholderia and Trichoderma) seem to be among microbes assisting plants to withstand abiotic stresses. This study sheds light on the efficient use of mWGS in the taxonomic assignment of soil microbes and in their response to watering. It also provides new avenues for improving biotic and abiotic resistance in domestic plant germplasm via the manipulation of soil microbes. Full article

Harnessing an ammonia-oxidizing microbiome has become an increasingly attractive form of management for mitigating greenhouse gas emissions in rice paddies; however, the relationship between greenhouse gas emissions and ammonia-oxidizing microbiomes, using a nitrogen application and irrigation regime, has not been well investigated. To decipher which of (and how) the specific mmonia-oxidizing bacterial species drive the greenhouse gas CH₄ and N₂O emissions, a field experiment with varying nitrogen application and irrigation regimes was initiated to investigate the succession of key bacterial consortia associated with GHG emissions. The results showed that water-saving irrigation (AWD) significantly increased NO₃-N and NH₄⁺-N concentrations, compared with conventional irrigation (FDF), whereas (total nitrogen) TN was little higher in FDF (1.38 g kg⁻¹) compared with the AWD (1.36 g kg⁻¹). During the rice-growing season, CH₄ emissions ascended speedily, and emissions peaked at maximum values of 3.32 and 4.41 ug mg⁻² h⁻¹ on day 5 in FDF and AWD irrigation regimes, respectively, and then they rapidly decreased during the midseason period, maintaining a relatively low emission rate until the rice was harvested. The patterns of N₂O emission fluxes had the same tendencies with N fertilization. Putative key taxa, such as Flavobacterium, Massilia, Arenimonas, Novosphingobium, Pseudomonas, exhibited significant positive relationships with higher GHG emissions, suggesting that they make particularly obvious contributions to N₂O emissions. These putative taxa should be considered when designing a high nitrogen application and irrigation strategy. As such, the nitrogen application of N180, and the irrigation regimes of water-saving irrigation, are recommended methods for N conservation and the mitigation of greenhouse gas emissions in rice paddies. Full article

The conversion of forests could change soil characteristics and, in turn, impact the microbial community. However, the long-term effect of forest transformation on bacterial and archaeal composition and diversity, especially on nitrogen functional communities, is poorly understood. This study aimed to explore the response of soil bacterial and archaeal communities, as well as nitrogen functional groups, to the conversion from natural broadleaved forests to Chinese fir (Cunninghamia lanceolate (Lamb.) Hook.) plantations in subtropical China by 16S rRNA amplicon sequencing. Except for soil bulk density (BD) and ammonium nitrogen (NH₄⁺–N) content, other soil properties all decreased with the conversion from natural forests to plantations. Alpha diversity of bacteria and archaea declined with the transformation from natural forests to plantations. The composition of bacteria and archaea was significantly different between natural forests and plantations, which could be mainly attributed to the change in the content of soil organic carbon (SOC), total nitrogen (TN), nitrate nitrogen (NO₃⁻–N), and available phosphorus (AP). The conversion of natural forests to plantations decreased the gene copies of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nifH (nitrogen fixation function) but increased denitrification gene copies (i.e., nirS, nirK, and nosZ). In summary, our study emphasizes the long-term negative effect of the conversion from natural broadleaved forests into Chinese fir plantations on the diversity and richness of soil microbial communities, thereby deeply impacting the cycling of soil nitrogen. Full article

Here, we investigated the impact of different turning frequency (TF) on dynamic changes of N fractions, NH₃ emission and bacterial/archaeal community during chicken manure composting. Compared to higher TF (i.e., turning every 1 or 3 days in CMS1 or CMS3 treatments, respectively), lower TF (i.e., turning every 5 or 7 days in CMS5 or CMS7 treatments, respectively) decreased NH₃ emission by 11.42–18.95%. Compared with CMS1, CMS3 and CMS7 treatments, the total nitrogen loss of CMS5 decreased by 38.03%, 17.06% and 24.76%, respectively. Ammonia oxidizing bacterial/archaeal (AOB/AOA) communities analysis revealed that the relative abundance of Nitrosospira and Nitrososphaera was higher in lower TF treatment during the thermophilic and cooling stages, which could contribute to the reduction of NH₃ emission. Thus, different TF had a great influence on NH₃ emission and microbial community during composting. It is practically feasible to increase the abundance of AOB/AOA through adjusting TF and reduce NH₃ emission the loss of nitrogen during chicken manure composting. Full article

The impact of polymer-based slow-release urea formulations on soil microbial N dynamics in potatoes has been sparingly deciphered. The present study investigated the effect of a biodegradable nano-polymer urea formulation on soil enzymatic activities and microflora involved in the N cycling of potato (Solanum tuberosum L.). The nano-chitosan-urea composite (NCUC) treatment significantly increased the soil dehydrogenase activity, organic carbon content and available potassium compared to the conventional urea (CU) treatment. The soil ammonical nitrogen (NH₄⁺-N) and nitrate nitrogen (NO₃⁻-N) contents and urease activity were significantly decreased in the NCUC-amended soil. The slow urea hydrolysis rate led to low concentrations of NH₄⁺-N and NO₃⁻-N in the tested potato soil. Furthermore, these results corroborate the low count of ammonia oxidizer and nitrate reducer populations. Quantitative PCR (q-PCR) studies revealed that the relative abundance of eubacterial (AOB) and archaeal ammonia-oxidizing (AOA) populations was reduced in the NCUC-treated soil compared to CU. The abundance of AOA was particularly lower than AOB, probably due to the more neutral and alkaline conditions of the tested soil. Our results suggest that the biodegradable polymer urea composite had a significant effect on the microbiota associated with soil N dynamics. Therefore, the developed NCUC could be used as a slow N-release fertilizer for enhanced growth and crop yields of potato. Full article

Urban development is one of the leading causes of biodiversity change. Understanding how soil microorganisms respond to urbanization is particularly important because they are crucial for the provisioning of ecosystem functions and services. Here, we collected monthly soil samples over one year across three locations representing an urbanization gradient (low-moderate-high) in the arid Southwestern USA, and we characterized their microbial communities using marker gene sequencing. Our results showed that microbial richness and community composition exhibited nonsignificant changes over time regardless of the location. Soil fungal richness was lower in moderately and highly urbanized locations, but soil bacterial/archaeal richness was not significantly different among locations. Both bacteria/archaea and fungi exhibited significant differences in community composition across locations. After inferring potential functional groups, soils in the highly urbanized location had lower proportions of arbuscular mycorrhizal fungi and soil saprotrophic fungi but had higher proportions of bacterial taxa involved in aromatic compound degradation, human pathogens, and intracellular parasites. Furthermore, ammonia-oxidizing bacteria were more abundant in the highly urbanized location, but ammonia-oxidizing archaea were more abundant in lowly and moderately urbanized locations. Together, these results highlight the significant changes in belowground microbial communities across an urbanization gradient, and these changes might have important implications for aboveground–belowground interactions, nutrient cycling, and human health. Full article

Recent advancements in agricultural metagenomics allow for characterizing microbial indicators of soil health brought on by changes in management decisions, which ultimately affect the soil environment. Field-scale studies investigating the microbial taxa from agricultural experiments are sparse, with none investigating the long-term effect of crop rotation and tillage on microbial indicator species. Therefore, our goal was to determine the effect of rotations (continuous corn, CCC; continuous soybean, SSS; and each phase of a corn-soybean rotation, Cs and Sc) and tillage (no-till, NT; and chisel tillage, T) on the soil microbial community composition following 20 years of management. We found that crop rotation and tillage influence the soil environment by altering key soil properties, such as pH and soil organic matter (SOM). Monoculture corn lowered pH compared to SSS (5.9 vs. 6.9, respectively) but increased SOM (5.4% vs. 4.6%, respectively). Bacterial indicator microbes were categorized into two groups: SOM dependent and acidophile vs. N adverse and neutrophile. Fungi preferred the CCC rotation, characterized by low pH. Archaeal indicators were mainly ammonia oxidizers with species occupying niches at contrasting pHs. Numerous indicator microbes are involved with N cycling due to the fertilizer-rich environment, prone to aquatic or gaseous losses. Full article

Rapid urbanization has destroyed urban water systems and led to blackened and odorous rivers. The heavily polluted rivers are always facing eutrophication and heavy metal pollution, while the combined effects of these environmental factors on the microbial diversity and distribution of the river microbial communities have not been adequately reported, especially the archaeal communities. In this study, we investigated the community structure and microbial distribution of sediment archaeal communities from an urban blackened and odorous river basin of the Zhang river, in Nanling, China. Results showed that the archaeal community from the eight sediment sites have average values of Shannon and Chao1 at 3.4921 and 232.7202, respectively. The community diversity and richness were different among samples. Halobacterota and Euryarchaeota were the most abundant phylum and Crenarchaeota also took up a considerable amount of the archaeal community. To reveal the main environmental drivers of the distribution of archaeal communities in sediment, the environmental physicochemical factors (total nitrogen, total phosphorus, oxidation/reduction potential, nitrate nitrogen, ammonia nitrogen, pH and total organic carbon) and heavy metals (Cr, Ni, Cu, Zn, As, Cd, Pb and Hg) in sediment were determined. A redundancy analysis (RDA) revealed that Eh was the most prominent influencing factor, and As was the most influential heavy metal on the microbial distribution of archaeal communities. Furthermore, a variance partitioning analysis (VPA) was used to identify the impacts of physicochemical factors and heavy metals on the archaeal community distribution. Results showed that heavy metals have higher effects on archaeal community distribution than physicochemical factors. The present study suggested that the heavy metal pollution should be paid more attention in the microbial distribution in heavily polluted urban rivers, and also should be taken into consideration for improving the efficacies of ecological evaluation and remediation. Full article