The Ecology of Acidobacteria: Moving beyond Genes and Genomes

Comprehensive agricultural ecological effects of aeration on regenerated liquid fertilizer of mini flush toilet

The high concentration of organic waste liquid obtained from the mini flush pipeline discharge technology based on source separation has the potential for fertilizer utilization. However, there are concerns about the risk of secondary pollution. This study proposes the idea of aeration treatment for regenerated liquid fertilizers to induce beneficial changes in their material composition and properties. Initially, this study compares the characteristic changes in nitrogen transformation of liquid fertilizer through aeration treatment. Subsequently, it examines the effects of different types of liquid fertilizers on soil properties, plant physiology, and soil microbial communities. Finally, we elucidate the flow and distribution of nitrogen in soil, plants, and nitrogen-containing gas emissions in agricultural ecosystems through material flow accounting. The study found that aeration treatment can reduce the ammonia nitrogen ratio while increasing the proportions of nitrite nitrogen and nitrate nitrogen. The regenerated liquid fertilizer through aeration treatment not only significantly increased the chlorophyll, protein, and polysaccharide content of vegetable leaves (P < 0.05) but also reduced nitrate accumulation. Moreover, it can reduce the risk of soil nitrate nitrogen leaching and increase the diversity of soil bacterial communities, enhancing the ecological functions of bacteria involved in carbon and nitrogen cycling. Material flow accounting indicated that aeration treatment for liquid fertilizer could reduce gaseous nitrogen loss by 50.0 %, improve the nitrogen utilization efficiency of vegetables by 95.5 %, and enhance soil nitrogen retention by 11.4 %. Overall, the results show that aeration treatment can improve the agricultural utilization of liquid fertilizer and reduce the risk of secondary pollution, providing preliminary decision-making support for optimizing resource treatment strategies for mini-flush toilet fecal waste to realize the agricultural cycle.

Environmentally responsive changes in mucus indicators and microbiota of Chinese sturgeon Acipensersinensis

The impact of environmental factors on the health of the endangered Chinese sturgeon (Acipenser sinensis) and the potential hazards associated with sample collection for health monitoring pose urgent need to its conservation. In this study, Chinese sturgeons were selected from indoor and outdoor environments to evaluate metabolic and tissue damage indicators, along with a non-specific immune enzyme in fish mucus. Additionally, the microbiota of both water bodies and fish mucus were determined using 16S rRNA high-throughput sequencing. The correlation between the indicators and the microbiota was investigated, along with the measurement of multiple environmental factors. The results revealed significantly higher levels of two metabolic indicators, total protein (TP) and cortisol (COR) in indoor fish mucus compared to outdoor fish mucus (p < 0.05). The activities of acid phosphatase (ACP), alkaline phosphatase (ALP), creatine kinase (CK), alanine aminotransferase (ALT), aspartate aminotransferase (AST), and lactate dehydrogenase (LDH) were significantly higher in indoor fish, serving as indicators of tissue damage (p < 0.05). The activity of lysozyme (LZM) was significantly lower in indoor fish (p < 0.01). Biomarker analysis at the phylum and genus levels in outdoor samples revealed that microorganisms were primarily related to the catabolism of organic nutrients. In indoor environments, microorganisms displayed a broader spectrum of functions, including ecological niche establishment, host colonization, potential pathogenicity, and antagonism of pathogens. KEGG functional enrichment corroborated these findings. Dissolved oxygen (DO), electrical conductivity (EC), ammonia nitrogen (NH3-N), turbidity (TU), and chemical oxygen demand (COD) exerted effects on outdoor microbiota. Temperature (TEMP), nitrate (NO3-), total phosphorus (TP), and total nitrogen (TN) influenced indoor microbiota. Changes in mucus indicators, microbial structure, and function in both environments were highly correlated with these factors. Our study provides novel insights into the health impacts of different environments on Chinese sturgeon using a non-invasive method.

The resistance of hydrogenotrophic methanogenic microorganisms to ofloxacin in sludge anaerobic digestion process

Ofloxacin (OFL) is a commonly used antibiotic that can enter wastewater treatment plants and be adsorbed by the sludge, resulting in a high OFL concentration in sludge and affecting the subsequent sludge anaerobic digestion process. However, the micro mechanisms involved in this process have not been thoroughly studied. Therefore, this study focuses on the effect of OFL on the sludge anaerobic digestion of sludge to provide such support. The experimental results showed that the maximal methane yield decreased from 277.7 to 164.7 mL/g VSS with the OFL concentration increased from 0 to 300 mg/L. Additionally, OFL hindered the intermediate biochemical processes of hydrolysis, acidogenesis, acetogenesis, and acetoclastic methanogenesis. However, it promoted hydrogenotrophic methanogenesis process, using H2 as substrate, with the concentration of 300 mg/L OFL was 5.54 fold methane production of that in the control. Further investigation revealed that the negative effect of OFL was likely due to the induction of reactive oxygen species, which led to a decrease in cell activity and interference with the activity of key enzymes. Microbiological analysis revealed that OFL reduced the relative abundance of hydrolysis and acidogenesis bacteria, and Methanosaeta archaea, while increasing the relative abundance of hydrogenotrophic methanogenesis microorganism from 36.54% to 51.48% as the OFL concentration increase from 0 to 300 mg/L.

Nutrient limitation mediates soil microbial community structure and stability in forest restoration

Soil microorganisms are often limited by nutrients, representing an important control of heterotrophic metabolic processes. However, how nutrient limitations relate to microbial community structure and stability remains unclear, which creates a knowledge gap to understanding microbial biogeography and community changes during forest restoration. Here, we combined an eco-enzymatic stoichiometry model and high-throughput DNA sequencing to assess the potential roles of nutrient limitation on microbial community structure, assembly, and stability along a forest restoration sequence in the Qinling Mountains, China. Results showed that nutrient limitations tended to decrease during the oak forest restoration. Carbon and phosphorus limitations enhanced community dissimilarity and significantly increased bacterial alpha diversity, but not fungal diversity. Stochastic assembly processes primarily structured both bacterial (average contribution of 74.73 % and 74.17 % in bulk and rhizosheath soils, respectively) and fungal (average contribution of 77.23 % and 72.04 % in bulk and rhizosheath soils, respectively) communities during forest restoration, with nutrient limitation also contributing to the importance of stochastic processes in the bacterial communities. The migration rate (m) for bacteria was 0.19 and 0.23, respectively in both bulk soil and rhizosheath soil, and was greater than that for the fungi (m was 1.19 and 1.41, respectively), indicating a stronger dispersal limitation for fungal communities. Finally, nutrient limitations significantly affected bacterial and fungal co-occurrence with more interconnections occurring among weakly nutrient-limited microbial taxa and nutrient limitations reducing community stability when nutrient availability changed during forest restoration. Our findings highlight the fundamental effects of nutrient limitations on microbial communities and their self-regulation under changing environmental resources.

Environmentally relevant concentrations of microplastics from agricultural mulch and cadmium negatively impact earthworms by triggering neurotoxicity and disrupting homeostasis

Recent research has highlighted the ecological risk posed by microplastics (MPs) from mulching film and heavy metals to soil organisms. However, most studies overlooked real environmental levels of MPs and heavy metals. To address this gap, pristine and aged polyethylene (PE) mulching film-derived MPs (PMPs, 500 mg/kg; AMPs, 500 mg/kg) were combined with cadmium (Cd, 0.5 mg/kg) to assess the acute toxicity to earthworms and investigate associated molecular mechanisms (oxidative stress, osmoregulation pressure, gut microbiota, and metabolic responses) at environmentally relevant concentrations. Compared to Cd alone and Cd + PMPs treatments (11.15 ± 4.19 items/g), Cd + AMPs treatment resulted in higher MPs bioaccumulation (23.73 ± 13.14 items/g), more severe tissue lesions, and increased cell membrane osmotic pressure in earthworms' intestines. Cd + AMPs induced neurotoxicity through elevated levels of glutamate and acetylcholinesterase. Earthworm intestines (0.98 ± 0.49 to 3.33 ± 0.37 mg/kg) exhibited significantly higher Cd content than soils (0.19 ± 0.01 to 0.51 ± 0.06 mg/kg) and casts (0.15 ± 0.01 to 0.25 ± 0.05 mg/kg), indicating PE-MPs facilitated Cd transport in earthworms' bodies. Metabolomic analysis showed Cd + AMPs exposure depleted energy and nucleotide metabolites, disrupted cell homeostasis more profoundly than Cd and Cd + PMPs treatments. Overall, co-exposure to AMPs + Cd induced more severe neurotoxicity and disruption of homeostasis in earthworm than Cd and PMPs + Cd treatments. Our study, using Cd and MPs with environmental relevance, underscores MPs' role in amplifying Cd accumulation and toxicity in earthworms.

Effects of forest age and season on soil microbial communities in Chinese fir plantations

Understanding changes in the distribution patterns and diversity of soil microbial communities from the perspectives of age-related changes, seasonal variations, and the interaction between the two factors can facilitate the management of plantations. In Chinese fir plantations, we collected soils from different depths in over-mature forests, mature forests, near-mature forests, middle-aged forests, and young forests in summer, autumn, and winter in China's subtropical regions. As the forests developed, bacterial and fungal communities' diversity changed, reached a minimum value at near-mature forests, and then increased in mature forests or over-mature forests. Near-mature forests had the lowest topological properties. The Shannon index of microbial communities varied with seasonal changes (P < 0.05). Bacterial and fungal community composition at genus level was more closely related to temperature indicators (including daily average temperature, daily maximum temperature, and daily minimum temperature) (P < 0.01, 0.5554 < R2 <0.8185) than daily average precipitation (P > 0.05, 0.0321 < R2 <0.6773). Bacteria were clustered by season and fungi were clustered by forest age. We suggested that extending the tree cultivation time of plantations could promote microbial community recovery. In addition, we found some species worthy of attention, including Bacteroidetes in autumn in over-mature forests, and Firmicutes in summer in young forests.IMPORTANCEChinese fir [Cunninghamia lanceolata (Lamb.) Hook] is an important fast-growing species with the largest artificial forest area in China, with the outstanding problems of low quality in soil. Soil microorganisms play a crucial role in soil fertility by decomposing organic matter, optimizing soil structure, and releasing essential nutrients for plant growth. In order to maintain healthy soil quality and prevent nutrient depletion and land degradation, it is crucial to understand the changes of soil microbial composition and diversity. Our study determined to reveal the change of soil microbial community from stand age, season, and the interaction between the two aspects, which is helpful to understand how interannual changes in different years and seasonal changes in one year affect soil fertility restoration and sustainable forest plantation management. It is a meaningful exploration of soil microbial communities and provides new information for further research.

Treatment of low-C/N nitrate wastewater using a partial denitrification-anammox granule system: Granule reconstruction, stability, and microbial structure analyses

Industrial wastewater discharged into sewer systems is often characterized by high nitrate contents and low C/N ratios, resulting in high treatment costs when using conventional activated sludge methods. This study introduces a partial denitrification-anammox (PD/A) granular process to address this challenge. The PD/A granular process achieved an effluent TN level of 3.7 mg/L at a low C/N ratio of 2.3. Analysis of a typical cycle showed that the partial denitrification peaked within 15 min and achieved a nitrate-to-nitrite transformation ratio of 86.9%. Anammox, which was activated from 15 to 120 min, contributed 86.2% of the TN removal. The system exhibited rapid recovery from post-organic shock, which was attributed to significant increases in protein content within TB-EPS. Microbial dispersion and reassembly were observed after coexistence of the granules, with Thauera (39.12%) and Candidatus Brocadia (1.25%) identified as key functional microorganisms. This study underscores the efficacy of PD/A granular sludge technology for treating low-C/N nitrate wastewater.

Synergistic enhancement of cadmium immobilization and soil fertility through biochar and artificial humic acid-assisted microbial-induced calcium carbonate precipitation

Microbially induced carbonate precipitation (MICP) is emerging as a favorable alternative to traditional soil remediation techniques for heavy metals, primarily due to its environmental friendliness. However, a significant challenge in using MICP for farmland is not only to immobilize heavy metals but also to concurrently enhance soil fertility. This study explores the innovative combination of artificial humic acid (A-HA), biochar (BC), and Sporosarcina pasteurii (S. pasteurii) to mitigate the bioavailability of cadmium (Cd) in contaminated agricultural soils through MICP. X-ray diffraction (XRD) and scanning electron microscope (SEM) analyses revealed that the integration of BC and A-HA significantly enhances Cd immobilization efficiency by co-precipitating with CaCO3. Moreover, this treatment also improved soil fertility and ecological functions, as evidenced by increases in total nitrogen (TN, 9.0-78.2 %), alkaline hydrolysis nitrogen (AN, 259.7-635.5 %), soil organic matter (SOM, 18.1-27.9 %), total organic carbon (TOC, 43.8-48.8 %), dissolved organic carbon (DOC, 36.0-88.4 %) and available potassium (AK, 176.2-193.3 %). Additionally, the relative abundance of dominant phyla such as Proteobacteria and Firmicutes significantly increased with the introduction of BC and A-HA in MICP. Consequently, the integration of BC and A-HA with MICP offers a promising solution for remediating Cd-contaminated agricultural soil and synergistically enhancing soil fertility.

An inclusive study to elucidation the heavy metals-derived ecological risk nexus with antibiotic resistome functional shape of niche microbial community and their carbon substrate utilization ability in serpentine soil

Heavy metals (HMs) contained terrestrial ecosystems are often significantly display the antibiotic resistome in the pristine area due to increasing pressure from anthropogenic activity, is complex and emerging research interest. This study investigated that impact of chromium (Cr), nickel (Ni), cobalt (Co) concentrations in serpentine soil on the induction of antibiotic resistance genes and antimicrobial resistance within the native bacterial community as well as demonstrated their metabolic fingerprint. The full-length 16S-rRNA amplicon sequencing observed an increased abundance of Firmicutes, Actinobacteriota, and Acidobacteriota in serpentine soil. The microbial community in serpentine soil displayed varying preferences for different carbon sources, with some, such as carbohydrates and carboxylic acids, being consistently favored. Notably, 27 potential antibiotic resistance opportunistic bacterial genera have been identified in different serpentine soils. Among these, Lapillicoccus, Rubrobacter, Lacibacter, Chloroplast, Nitrospira, Rokubacteriales, Acinetobacter, Pseudomonas were significantly enriched in high and medium HMs concentrated serpentine soil samples. Functional profiling results illustrated that vancomycin resistance pathways were prevalent across all groups. Additionally, beta-lactamase, aminoglycoside, tetracycline, and vancomycin resistance involving specific bio-maker genes (ampC, penP, OXA, aacA, strB, hyg, aph, tet(A/B), otr(C), tet(M/O/Q), van(A/B/D), and vanJ) were the most abundant and enriched in the HMs-contaminated serpentine soil. Overall, this study highlighted that heavy-metal enriched serpentine soil is potential to support the proliferation of bacterial antibiotic resistance in native microbiome, and might able to spread antibiotic resistance to surrounding environment.

Different effects of seasonal impoundment and land use change on microbiome in a tributary sediment of the three gorgers reservoir

Anthropogenic activities significantly impact river ecosystem nutrient fluxes and microbial metabolism. Here, we examined the seasonal and spatial variation of sediments physicochemical parameters and the associated microbiome in the Pengxi river, a representative tributary of Three Gorges Reservoir, in response to seasonal impoundment and land use change by human activities. Results revealed that seasonal impoundment and land use change enhanced total organic carbon (TOC), total nitrogen (TN) and ammonium nitrogen (NH4+-N) concentration in the sediment, but have different effects on sediment microbiome. Sediment microbiota showed higher similarity during the seasonal high-water level (HWL) in consecutive two years. The abundant phyla Acidobacteria, Gemmatimonadetes, Cyanobacteria, Actinobacteria and Planctomycetes significantly increased as water level increased. Along the changes in bacterial taxa, we also observed changes in predicted carbon fixation functions and nitrogen-related functions, including the significantly higher levels of Calvin cycle, 4HB/3HP cycle, 3HP cycle and assimilatory nitrate reduction, while significantly lower level of denitrification. Though land use change significantly increased TOC, TN and NH4+-N concentration, its effects on spatial variation of bacterial community composition and predicted functions was not significant. The finding indicates that TGR hydrologic changes and land use change have different influences on the carbon and nitrogen fluxes and their associated microbiome in TGR sediments. A focus of future research will be on assessing on carbon and nitrogen flux balance and the associated carbon and nitrogen microbial cycling in TGR sediment.

Bacterial abundant taxa exhibit stronger environmental adaption than rare taxa in the Arctic Ocean sediments

Marine bacteria influence Earth's environmental dynamics in fundamental ways by controlling the biogeochemistry and productivity of the oceans. However, little is known about the survival strategies of their abundant and rare taxa, especially in polar marine environments. Here, bacterial environmental adaptation, community assembly processes, and co-occurrence patterns between abundant and rare taxa were compared in the Arctic Ocean sediments. Results indicated that the diversity of rare taxa is significantly higher than that of abundant taxa, whereas the distance-decay rate of rare taxa community similarity is over 1.5 times higher than that of abundant taxa. Furthermore, abundant taxa exhibited broader environmental breadth and stronger phylogenetic signals compared to rare taxa. Additionally, the community assembly processes of the abundant taxa were predominantly governed by 81% dispersal limitation, while rare taxa were primarily influenced by 48% heterogeneous selection. The co-occurrence network further revealed the abundant taxa formed a more complex network to enhance their environmental adaptability. This study revealed the differences in environmental responses and community assembly processes between bacterial abundant and rare taxa in polar ocean sediments, providing some valuable insights for understanding their environmental adaptation strategies in marine ecosystems.

Barley farmland harbors a highly homogeneous soil bacterial community compared to wild ecosystems in the Qinghai-Xizang Plateau

Introduction

Understanding patterns and processes of microbial biogeography in soils is important for monitoring ecological responses to human activities, particularly in ecologically vulnerable areas such as the Qinghai-Xizang Plateau. Highland barley is the staple food of local people and has mainly been cultivated along the Yarlung Zangbo River valley in Xizang.

Methods

Here we investigated soil bacterial communities from 33 sampling sites of highland barley farmland in this region and compared them to those from wild ecosystems including alpine tundra, meadow, forest, and swamp. Additionally, the effects of environmental factors on bacterial communities, as well as the relative importance of stochastic and deterministic processes in shaping the beta diversity of soil bacterial communities in alpine ecosystems were assessed.

Results

In contrast to soils of wild ecosystems, these farmland samples harbored a highly homogeneous bacterial community without significant correlations with geographic, elevation, and edaphic distances. Discriminant bacterial taxa identified for farmland samples belong to Acidobacteria, with Acidobacteria Gp4 as the dominant clade. Although Acidobacteria were the most abundant members in all ecosystems, characterized bacterial taxa of meadow and forest were members of other phyla such as Proteobacteria and Verrucomicrobia. pH and organic matter were major edaphic attributes shaping these observed patterns across ecosystems. Null model analyses revealed that the deterministic assembly was dominant in bacterial communities in highland barley farmland and tundra soils, whereas stochastic assembly also contributed a large fraction to the assembly of bacterial communities in forest, meadow and swamp soils.

Discussion

These findings provide an insight into the consequences of human activities and agricultural intensification on taxonomic homogenization of soil bacterial communities in the Qinghai-Xizang Plateau.

Modulation of the gut microbiota by processed food and natural food: evidence from the Siniperca chuatsi microbiome

Habitual dietary changes have the potential to induce alterations in the host's gut microbiota. Mandarin fish (Siniperca chuatsi), an aquatic vertebrate species with distinct feeding habits, were fed with natural feeds (NF) and artificial feeds (AF) to simulate the effects of natural and processed food consumption on host gut microbiota assemblages. The results showed that the alpha diversity index was reduced in the AF diet treatment, as lower abundance and diversity of the gut microbiota were observed, which could be attributed to the colonized microorganisms of the diet itself and the incorporation of plant-derived proteins or carbohydrates. The β-diversity analysis indicated that the two dietary treatments were associated with distinct bacterial communities. The AF diet had a significantly higher abundance of Bacteroidota and a lower abundance of Actinomycetota, Acidobacteriota, and Chloroflexota compared to the NF group. In addition, Bacteroidota was the biomarker in the gut of mandarin fish from the AF treatment, while Acidobacteriota was distinguished in the NF treatments. Additionally, the increased abundance of Bacteroidota in the AF diet group contributed to the improved fermentation and nutrient assimilation, as supported by the metabolic functional prediction and transcriptome verification. Overall, the present work used the mandarin fish as a vertebrate model to uncover the effects of habitual dietary changes on the evolution of the host microbiota, which may provide potential insights for the substitution of natural foods by processed foods in mammals.

Irons differently modulate bacterial guilds for leading to varied efficiencies in simultaneous nitrification and denitrification (SND) within four aerobic bioreactors

As a novel biological wastewater nitrogen removal technology, simultaneous nitrification and denitrification (SND) has gained increasing attention. Iron, serving as a viable material, has been shown to influence nitrogen removal. However, the precise impact of iron on the SND process and microbiome remains unclear. In this study, bioreactors amended with iron of varying valences were evaluated for total nitrogen (TN) removal efficiencies under aerobic conditions. The acclimated control reactor without iron addition (NCR) exhibited high ammonia nitrogen (AN) removal efficiency (98.9%), but relatively low TN removal (78.6%) due to limited denitrification. The reactor containing zero-valent iron (Fe0R) demonstrated the highest SND rate of 92.3% with enhanced aerobic denitrification, albeit with lower AN removal (84.1%). Significantly lower SND efficiencies were observed in reactors with ferrous (Fe2R, 66.3%) and ferric (Fe3R, 58.2%) iron. Distinct bacterial communities involved in nitrogen metabolisms were detected in these bioreactors. The presence of complete ammonium oxidation (comammox) genus Nitrospira and anammox bacteria Candidatus Brocadia characterized efficient AN removal in NCR. The relatively low abundance of aerobic denitrifiers in NCR hindered denitrification. Fe0R exhibited highly abundant but low-efficiency methanotrophic ammonium oxidizers, Methylomonas and Methyloparacoccus, along with diverse aerobic denitrifiers, resulting in lower AN removal but an efficient SND process. Conversely, the presence of Fe2+/Fe3+ constrained the denitrifying community, contributing to lower TN removal efficiency via inefficient denitrification. Therefore, different valent irons modulated the strength of nitrification and denitrification through the assembly of key microbial communities, providing insight for microbiome modulation in nitrogen-rich wastewater treatment.

Biosynthetic potential of uncultured anammox community bacteria revealed through multi-omics analysis

Microbial secondary metabolites (SMs) and their derivatives have been widely used in medicine, agriculture, and energy. Growing needs for renewable energy and the challenges posed by antibiotic resistance, cancer, and pesticides emphasize the crucial hunt for new SMs. Anaerobic ammonium-oxidation (anammox) systems harbor many uncultured or underexplored bacteria, representing potential resources for discovering novel SMs. Leveraging HiFi long-read metagenomic sequencing, 1,040 biosynthetic gene clusters (BGCs) were unearthed from the anammox microbiome with 58% being complete and showcasing rich diversity. Most of them showed distant relations to known BGCs, implying novelty. Members of the underexplored lineages (Chloroflexota and Planctomycetota) and Proteobacteria contained lots of BGCs, showcasing substantial biosynthetic potential. Metaproteomic results indicated that Planctomycetota members harbored the most active BGCs, particularly those involved in producing potential biofuel-ladderane. Overall, these findings underscore that anammox microbiomes could serve as valuable resources for mining novel BGCs and discovering new SMs for practical application.

Global soil metagenomics reveals distribution and predominance of Deltaproteobacteria in nitrogen-fixing microbiome

BACKGROUND

Biological nitrogen fixation is a fundamental process sustaining all life on earth. While distribution and diversity of N2-fixing soil microbes have been investigated by numerous PCR amplicon sequencing of nitrogenase genes, their comprehensive understanding has been hindered by lack of de facto standard protocols for amplicon surveys and possible PCR biases. Here, by fully leveraging the planetary collections of soil shotgun metagenomes along with recently expanded culture collections, we evaluated the global distribution and diversity of terrestrial diazotrophic microbiome.

RESULTS

After the extensive analysis of 1,451 soil metagenomic samples, we revealed that the Anaeromyxobacteraceae and Geobacteraceae within Deltaproteobacteria are ubiquitous groups of diazotrophic microbiome in the soils with different geographic origins and land usage types, with particular predominance in anaerobic soils (paddy soils and sediments).

CONCLUSION

Our results indicate that Deltaproteobacteria is a core bacterial taxon in the potential soil nitrogen fixation population, especially in anaerobic environments, which encourages a careful consideration on deltaproteobacterial diazotrophs in understanding terrestrial nitrogen cycling. Video Abstract.

Changes in Rumen Microbiology and Metabolism of Tibetan Sheep with Different Lys/Met Ratios in Low-Protein Diets

In ruminants, supplementing appropriate amounts of amino acids improves growth, feed utilization efficiency, and productivity. This study aimed to assess the effects of different Lys/Met ratios on the ruminal microbial community and the metabolic profiling in Tibetan sheep using 16S rDNA sequencing and non-target metabolomics. Ninety-two-month-old Tibetan rams (initial weight = 15.37 ± 0.92 kg) were divided into three groups and fed lysine/methionine (Lys/Met) of 1:1 (LP-L), 2:1 (LP-M), and 3:1 (LP-H) in low-protein diet, respectively. Results: The T-AOC, GSH-Px, and SOD were significantly higher in the LP-L group than in LP-H and LP-M groups (p < 0.05). Cellulase activity was significantly higher in the LP-L group than in the LP-H group (p < 0.05). In the fermentation parameters, acetic acid concentration was significantly higher in the LP-L group than in the LP-H group (p < 0.05). Microbial sequencing analysis showed that Ace and Chao1 indicators were significantly higher in LP-L than in LP-H and LP-M (p < 0.05). At the genus level, the abundance of Rikenellaceae RC9 gut group flora and Succiniclasticum were significantly higher in LP-L than in LP-M group (p < 0.05). Non-target metabolomics analyses revealed that the levels of phosphoric acid, pyrocatechol, hydrocinnamic acid, banzamide, l-gulono-1,4-lactone, cis-jasmone, Val-Asp-Arg, and tropinone content were higher in LP-L. However, l-citrulline and purine levels were lower in the LP-L group than in the LP-M and LP-H groups. Banzamide, cis-jasmone, and Val-Asp-Arg contents were positively correlated with the phenotypic contents, including T-AOC, SOD, and cellulase. Phosphoric acid content was positively correlated with cellulase and lipase activities. In conclusion, the Met/Lys ratio of 1:1 in low-protein diets showed superior antioxidant status and cellulase activity in the rumen by modulating the microbiota and metabolism of Tibetan sheep.

Incidence of resistance to ALS and ACCase inhibitors in Echinochloa species and soil microbial composition in Northern Italy

The increasing amount of weeds surviving herbicide represents a very serious problem for crop management. The interaction between microbial community of soil and herbicide resistance, along with the potential evolutive consequences, are still poorly known and need to be investigated to better understand the impact on agricultural management. In our study, we analyzed the microbial composition of soils in 32 farms, located in the Northern Italy rice-growing area (Lombardy) with the aim to evaluate the relationship between the microbial composition and the incidence of resistance to acetolactate synthase (ALS) and acetyl-CoA carboxylase (ACCase) inhibiting herbicides in Echinochloa species. We observed that the coverage of weeds survived herbicide treatment was higher than 60% in paddy fields with a low microbial biodiversity and less than 5% in those with a high microbial biodiversity. Fungal communities showed a greater reduction in richness than Bacteria. In soils with a reduced microbial diversity, a significant increase of some bacterial and fungal orders (i.e. Lactobacillales, Malasseziales and Diaporthales) was observed. Interestingly, we identified two different microbial profiles linked to the two conditions: high incidence of herbicide resistance (H-HeR) and low incidence of herbicide resistance (L-HeR). Overall, the results we obtained allow us to make hypotheses on the greater or lesser probability of herbicide resistance occurrence based on the composition of the soil microbiome and especially on the degree of biodiversity of the microbial communities.

Decoupling between the genetic potential and the metabolic regulation and expression in microbial organic matter cleavage across microbiomes

Metagenomics, metatranscriptomics, and metaproteomics are used to explore the microbial capability of enzyme secretion, but the links between protein-encoding genes and corresponding transcripts/proteins across ecosystems are underexplored. By conducting a multi-omics comparison focusing on key enzymes (carbohydrate-active enzymes [CAZymes] and peptidases) cleaving the main biomolecules across distinct microbiomes living in the ocean, soil, and human gut, we show that the community structure, functional diversity, and secretion mechanisms of microbial secretory CAZymes and peptidases vary drastically between microbiomes at metagenomic, metatranscriptomic, and metaproteomic levels. Such variations lead to decoupled relationships between CAZymes and peptidases from genetic potentials to protein expressions due to the different responses of key players toward organic matter sources and concentrations. Our results highlight the need for systematic analysis of the factors shaping patterns of microbial cleavage on organic matter to better link omics data to ecosystem processes.

IMPORTANCE

Omics tools are used to explore adaptive mechanism of microbes in diverse systems, but the advantages and limitations of different omics tools remain skeptical. Here, we reported distinct profiles in microbial secretory enzyme composition revealed by different omics methods. In general, the predicted function from metagenomic analysis decoupled from the expression of corresponding transcripts/proteins. Linking omics results to taxonomic origin, functional capability, substrate specificity, secretion preference, and enzymatic activity measurement suggested the substrate's source, concentration and stoichiometry impose strong filtering on the expression of extracellular enzymes, which may overwrite the genetic potentials. Our results present an integrated perspective on the need for multi-dimensional characterization of microbial adaptation in a changing environment.

Origin and modern microbial ecology of secondary mineral deposits in Lehman Caves, Great Basin National Park, NV, USA

Lehman Caves is an extensively decorated high desert cave that represents one of the main tourist attractions in Great Basin National Park, Nevada. Although traditionally considered a water table cave, recent studies identified abundant speleogenetic features consistent with a hypogenic and, potentially, sulfuric acid origin. Here, we characterized white mineral deposits in the Gypsum Annex (GA) passage to determine whether these secondary deposits represent biogenic minerals formed during sulfuric acid corrosion and explored microbial communities associated with these and other mineral deposits throughout the cave. Powder X-ray diffraction (pXRD), scanning electron microscopy with electron dispersive spectroscopy (SEM-EDS), and electron microprobe analyses (EPMA) showed that, while most white mineral deposits from the GA contain gypsum, they also contain abundant calcite, silica, and other phases. Gypsum and carbonate-associated sulfate isotopic values of these deposits are variable, with δ34SV-CDT between +9.7‰ and +26.1‰, and do not reflect depleted values typically associated with replacement gypsum formed during sulfuric acid speleogenesis. Petrographic observations show that the sulfates likely co-precipitated with carbonate and SiO2 phases. Taken together, these data suggest that the deposits resulted from later-stage meteoric events and not during an initial episode of sulfuric acid speleogenesis. Most sedimentary and mineral deposits in Lehman Caves have very low microbial biomass, with the exception of select areas along the main tour route that have been impacted by tourist traffic. High-throughput 16S rRNA gene amplicon sequencing showed that microbial communities in GA sediments are distinct from those in other parts of the cave. The microbial communities that inhabit these oligotrophic secondary mineral deposits include OTUs related to known ammonia-oxidizing Nitrosococcales and Thaumarchaeota, as well as common soil taxa such as Acidobacteriota and Proteobacteria. This study reveals microbial and mineralogical diversity in a previously understudied cave and expands our understanding of the geomicrobiology of desert hypogene cave systems.

Metagenomic investigations into the microbial consortia, degradation pathways, and enzyme systems involved in the biodegradation of plastics in a tropical lentic pond sediment

The exploitation of exciting features of plastics for diverse applications has resulted in significant plastic waste generation, which negatively impacts environmental compartments, metabolic processes, and the well-being of aquatic ecosystems biota. A shotgun metagenomic approach was deployed to investigate the microbial consortia, degradation pathways, and enzyme systems involved in the degradation of plastics in a tropical lentic pond sediment (APS). Functional annotation of the APS proteome (ORFs) using the PlasticDB database revealed annotation of 1015 proteins of enzymes such as depolymerase, esterase, lipase, hydrolase, nitrobenzylesterase, chitinase, carboxylesterase, polyesterase, oxidoreductase, polyamidase, PETase, MHETase, laccase, alkane monooxygenase, among others involved in the depolymerization of the plastic polymers. It also revealed that polyethylene glycol (PEG), polyhydroxyalkanoates (PHA), polyhydroxybutyrate (PHB), polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), polyethylene terephthalate (PET), and nylon have the highest number of annotated enzymes. Further annotation using the KEGG GhostKOALA revealed that except for terephthalate, all the other degradation products of the plastic polymers depolymerization such as glyoxylate, adipate, succinate, 1,4-butanediol, ethylene glycol, lactate, and acetaldehyde were further metabolized to intermediates of the tricarboxylic acid cycle. Taxonomic characterization of the annotated proteins using the AAI Profiler and BLASTP revealed that Pseudomonadota members dominate most plastic types, followed by Actinomycetota and Acidobacteriota. The study reveals novel plastic degraders from diverse phyla hitherto not reported to be involved in plastic degradation. This suggests that plastic pollution in aquatic environments is prevalent with well-adapted degrading communities and could be the silver lining in mitigating the impacts of plastic pollution in aquatic environments.

Resistance of soil bacterial communities from montane heathland ecosystems in the Cantabrian mountains (NW Spain) to a gradient of experimental nitrogen deposition

Elevated atmospheric nitrogen (N) deposition on terrestrial ecosystems has become one of the most important drivers of microbial diversity loss on a global scale, and has been reported to alter the soil function of nutrient-poor, montane Calluna vulgaris heathlands in the context of global change. In this work we analyze for the first time the shifts of bacterial communities in response to experimental addition of N in Calluna heathlands as a simulation of atmospheric deposition. Specifically, we evaluated the effects of five N addition treatments (0, 10, 20, and 50 kg N ha-1 yr-1 for 3-years; and 56 kg N ha-1 yr-1 for 10-years) on the resistance of soil bacterial communities as determined by changes in their composition and alpha and beta diversities. The study was conducted in montane Calluna heathlands at different development stages (young and mature phases) in the southern side of the Cantabrian Mountains (NW Spain). Our results evidenced a substantial increase of long-term (10-years) N inputs on soil extractable N-NH4+, particularly in young Calluna stands. The alpha diversity of soil bacterial communities in mature Calluna stands did not show a significant response to experimental N addition, whereas it was significantly higher under long-term chronic N addition (56 kg N ha-1 yr-1 for 10-years) in young Calluna stands. These bacterial community shifts are mainly attributable to a decrease in the dominance of Acidobacteria phylum, the most representative in montane Calluna ecosystems, in favor of copiotrophic taxa such as Actinobacteria or Proteobacteria phyla, favored under increased N availability. Future research should investigate what specific ecosystem functions performed by soil bacterial communities may be sensitive to increased nitrogen depositions, which may have substantial implications for the understanding of montane Calluna ecosystems' stability.

High microbiome and metabolome diversification in coexisting sponges with different bio-ecological traits

Marine Porifera host diverse microbial communities, which influence host metabolism and fitness. However, functional relationships between sponge microbiomes and metabolic signatures are poorly understood. We integrate microbiome characterization, metabolomics and microbial predicted functions of four coexisting Mediterranean sponges -Petrosia ficiformis, Chondrosia reniformis, Crambe crambe and Chondrilla nucula. Microscopy observations reveal anatomical differences in microbial densities. Microbiomes exhibit strong species-specific trends. C. crambe shares many rare amplicon sequence variants (ASV) with the surrounding seawater. This suggests important inputs of microbial diversity acquired by selective horizontal acquisition. Phylum Cyanobacteria is mainly represented in C. nucula and C. crambe. According to putative functions, the microbiome of P. ficiformis and C. reniformis are functionally heterotrophic, while C. crambe and C. nucula are autotrophic. The four species display distinct metabolic profiles at single compound level. However, at molecular class level they share a "core metabolome". Concurrently, we find global microbiome-metabolome association when considering all four sponge species. Within each species still, sets of microbe/metabolites are identified driving multi-omics congruence. Our findings suggest that diverse microbial players and metabolic profiles may promote niche diversification, but also, analogous phenotypic patterns of "symbiont evolutionary convergence" in sponge assemblages where holobionts co-exist in the same area.

Responses of soil microbiome to copper-based materials (nano and bulk) for agricultural applications: An indoor-mesocosm experiment

The foreseen increasing application of copper-based nanomaterials (Cu-NMs), replacing or complementing existing Cu-agrochemicals, may negatively impact the soil microbiome. Thus, we studied the effects on soil microbiome function and composition of nano copper oxide (nCuO) or copper hydroxide NMs in a commercial (Kocide®3000) or a lab-synthetized formulation (nCu(OH)2) or bulk copper hydroxide (Cu(OH)2-B), at the commonly recommended Cu dose of 50 mg(Cu)kg-1 soil. Microbial responses were studied over 28 days in a designed indoor mesocosm. On day-28, in comparison to non-treated soil (CT), all Cu-treatments led to a reduction in dehydrogenase (95% to 68%), arylsulfatase (41% to 27%), and urease (40% to 20%) activity. There was a 32% increase in the utilization of carbon substrates in the nCuO-treatment and an increased abundance of viable bacteria in the nCu(OH)2-treatment (75% of heterotrophic and 69% of P-solubilizing bacteria). The relative abundance of Acidobacteria [Kocide®3000, nCuO, and Cu(OH)2-B treatments] and Flavobacteriia [nCu(OH)2-treatment] was negatively affected by Cu exposure. The abundance of Cu-tolerant bacteria increased in soils treated with Kocide®3000 (Clostridia) and nCu(OH)2 (Gemmatimonadetes). All Cu-treated soils exhibited a reduced abundance of denitrification-related genes (0.05% of nosZ gene). The DTPA-extractable pool of ionic Cu(II) varied among treatments: Cu(OH)2-B > Kocide®3000 ∼ nCuO>nCu(OH)2, which may explain changes on the soil microbiome composition, at the genera and OTU levels. Thus, our study revealed that Cu-materials (nano and bulk) influence the soil microbiome with implications on its ecological role. It highlights the importance of assessing the impact of Cu-materials under dynamic and complex exposure scenarios and emphasizes the need for specific regulatory frameworks for NMs.

Soil bacteria and fungi communities are shaped by elevation influences in Colombian forest and páramo natural ecosystems

The influence of elevation on natural terrestrial ecosystems determines the arrangements of microbial communities in soils to be associated with biotic and abiotic factors. To evaluate changes of fungi and bacteria at the community level along an elevational gradient (between 1000 and 3800 m.a.s.l.), physicochemical measurements of soils, taxonomic identifications of plants, and metabarcoding sequences of the 16S rRNA gene for bacteria and the ITS1 region for fungi were obtained. The bacterial taxonomic composition showed that Acidobacteriota increased in abundance with elevation, while Actinobacteriota and Verrucomicrobiota decreased. Furthermore, Firmicutes and Proteobacteria maintained maximum levels of abundance at intermediate elevations (1200 and 2400 m.a.s.l.). In fungi, Ascomycota was more abundant at higher elevations, Basidiomycota tended to dominate at lower elevations, and Mortierellomycota had a greater presence at intermediate sites. These results correlated with the edaphic parameters of decreasing pH and increasing organic carbon and available nitrogen with elevation. In addition, the Shannon index found a greater diversity in bacteria than fungi, but both showed a unimodal pattern with maximum values in the Andean Forest at 2400 m.a.s.l. Through the microbial characterization of the ecosystems, the elevational gradient, soil properties, and vegetation were found to exert significant effects on microbial communities and alpha diversity indices. We conclude that the most abundant soil microorganisms at the sampling points differed in abundance and diversity according to the variations in factors influencing ecological communities.

Response of the metabolic activity and taxonomic composition of bacterial communities to mosaically varying soil salinity and alkalinity

Soil salinity and sodicity is a worldwide problem that affects the composition and activity of bacterial communities and results from elevated salt and sodium contents. Depending on the degree of environmental pressure and the combined effect of other factors, haloalkalitolerant and haloalkaliphilic bacterial communities will be selected. These bacteria play a potential role in the maintenance and restoration of salt-affected soils; however, until recently, only a limited number of studies have simultaneously studied the bacterial diversity and activity of saline-sodic soils. Soil samples were collected to analyse and compare the taxonomic composition and metabolic activity of bacteria from four distinct natural plant communities at three soil depths corresponding to a salinity‒sodicity gradient. Bacterial diversity was detected using 16S rRNA gene Illumina MiSeq amplicon sequencing. Community-level physiological profiles (CLPPs) were analysed using the MicroResp™ method. The genus-level bacterial composition and CLPPs differed significantly in soils with different alkaline vegetation. The surface soil samples also significantly differed from the intermediate and deep soil samples. The results showed that the pH, salt content, and Na+ content of the soils were the main edaphic factors influencing both bacterial diversity and activity. With salinity and pH, the proportion of the phylum Gemmatimonadota increased, while the proportions of Actinobacteriota and Acidobacteriota decreased.

The impacts of microplastics on the cycling of carbon and nitrogen in terrestrial soil ecosystems: Progress and prospects

As contaminants of emerging concern, microplastics (MPs) are ubiquitously present in almost all environmental compartments of the earth, with terrestrial soil ecosystems as the major sink for these contaminants. The accumulation of MPs in the soil can trigger a wide range of effects on soil physical, chemical, and microbial properties, which may in turn cause alterations in the biogeochemical processes of some key elements, such as carbon and nitrogen. Until recently, the effects of MPs on the cycling of carbon and nitrogen in terrestrial soil ecosystems have yet to be fully understood, which necessitates a review to summarize the current research progress and propose suggestions for future studies. The presence of MPs can affect the contents and forms of soil carbon and nitrogen nutrients (e.g., total and dissolved organic carbon, dissolved organic nitrogen, NH4+-N, and NO3--N) and the emissions of CH4, CO2, and N2O by altering soil microbial communities, functional gene expressions, and enzyme activities. Exposure to MPs can also affect plant growth and physiological processes, consequently influencing carbon fixation and nitrogen uptake. Specific effects of MPs on carbon and nitrogen cycling and the associated microbial parameters can vary considerably with MP properties (e.g., dose, polymer type, size, shape, and aging status) and soil types, while the mechanisms of interaction between MPs and soil microbes remain unclear. More comprehensive studies are needed to narrow the current knowledge gaps.

Integrated management of fruit trees and Bletilla striata: implications for soil nutrient profiles and microbial community structures

Introduction

Forest medicinal compound systems in agroforestry ecosystems represent a multi-layered cultivation approach that utilizes forest resources efficiently. However, research on how these systems affect soil nutrients and microbial communities is limited.

Methods

This study compared the soil chemical properties and microbial communities of Bletilla striata (C) grown alone versus in agroforestry systems with apple (PB), pear (LB), and peach trees (TB), aiming to understand the impact of these systems on soil health and microbial diversity.

Results

Soil in the GAB systems showed increased levels of essential nutrients but lower pH and ammonium nitrogen levels compared to the control. Significant improvements in organic matter, total phosphorus, and total potassium were observed in TB, PB, and LB systems, respectively. The bacterial diversity increased in GAB systems, with significant changes in microbial phyla indicative of a healthier soil ecosystem. The correlation between soil properties and bacterial communities was stronger than with fungal communities.

Discussion

Integrating B. striata with fruit trees enhances soil nutrients and microbial diversity but may lead to soil acidification. Adjustments such as using controlled-release fertilizers and soil amendments like lime could mitigate negative impacts, improving soil health in GAB systems.

Organic farming promotes the abundance of fungi keystone taxa in bacteria-fungi interkingdom networks

Soil bacteria-fungi interactions are essential in the biogeochemical cycles of several nutrients, making these microbes major players in agroecosystems. While the impact of the farming system on microbial community composition has been extensively reported in the literature, whether sustainable farming approaches can promote associations between bacteria and fungi is still unclear. To study this, we employed 16S, ITS, and 18S DNA sequencing to uncover how microbial interactions were affected by conventional and organic farming systems on maize crops. The Bray-Curtis index revealed that bacterial, fungal, and arbuscular mycorrhizal fungi communities were significantly different between the two farming systems. Several taxa known to thrive in healthy soils, such as Nitrosophaerales, Orbiliales, and Glomus were more abundant in the organic farming system. Constrained ordination revealed that the organic farming system microbial community was significantly correlated with the β-glucosidase activity, whereas the conventional farming system microbial community significantly correlated with soil pH. Both conventional and organic co-occurrence interkingdom networks exhibited a parallel node count, however, the former had a higher number of edges, thus being denser than the latter. Despite the similar amount of fungal nodes in the co-occurrence networks, the organic farming system co-occurrence network exhibited more than 3-fold the proportion of fungal taxa as keystone nodes than the conventional co-occurrence network. The genera Bionectria, Cercophora, Geastrum, Penicillium, Preussia, Metarhizium, Myceliophthora, and Rhizophlyctis were among the fungal keystone nodes of the organic farming system network. Altogether, our results uncover that beyond differences in microbial community composition between the two farming systems, fungal keystone nodes are far more relevant in the organic farming system, thus suggesting that bacteria-fungi interactions are more frequent in organic farming systems, promoting a more functional microbial community.

Effects of running time on biological activated carbon filters: water purification performance and microbial community evolution

Ozone-biologically activated carbon (BAC) filtration is an advanced treatment process that can be applied to remove recalcitrant organic micro-pollutants in drinking water treatment plants (DWTPs). In this study, we continuously monitored a new and an old BAC filter in a DWTP for 1 year to compare their water purification performance and microbial community evolution. The results revealed that, compared with the new filter, the use of the old BAC filter facilitated a slightly lower rate of dissolved organic carbon (DOC) removal. In the case of the new BAC filter, we recorded general increases in the biomass and microbial diversity of the biofilm with a prolongation of operating time, with the biomass stabilizing after 7 months. For both new and old BAC filters, Proteobacteria and Acidobacteria were the dominant bacterial phyla. At the genus level, the microbial community gradually shifted over the course of operation from a predominance of Herminiimonas and Hydrogenophaga to one predominated by Bradyrhizbium, Bryobacter, Hyphomicrobium, and Pedomicrobium, with Bradyrhizobium being established as the most abundant genus in the old BAC filter. Regarding spatial distribution, we detected reductions in the biomass and number of operational taxonomic units with increasing biofilm depth, whereas there was a corresponding increase in microbial diversity. However, compared with the effects of time, the influence of depth on the composition of the biofilm microbial community was considerably smaller. Furthermore, co-occurrence network analysis revealed that the microbial community network of the new filter after 11 months of operation was the most tightly connected, although its modular coefficient was the lowest of those assessed. We speculate that the positive and negative interactions within the network may be attributable to symbiotic or competitive relationships among species. Moreover, there may have been a significant negative interaction between SWB02 and Acidovorax, plausibly associated with a competition for substrates.

Drivers and human impacts on topsoil bacterial and fungal community biogeography across Australia

Soil microbial diversity mediates a wide range of key processes and ecosystem services influencing planetary health. Our knowledge of microbial biogeography patterns, spatial drivers and human impacts at the continental scale remains limited. Here, we reveal the drivers of bacterial and fungal community distribution in Australian topsoils using 1384 soil samples from diverse bioregions. Our findings highlight that climate factors, particularly precipitation and temperature, along with soil properties, are the primary drivers of topsoil microbial biogeography. Using random forest machine-learning models, we generated high-resolution maps of soil bacteria and fungi across continental Australia. The maps revealed microbial hotspots, for example, the eastern coast, southeastern coast, and west coast were dominated by Proteobacteria and Acidobacteria. Fungal distribution is strongly influenced by precipitation, with Ascomycota dominating the central region. This study also demonstrated the impact of human modification on the underground microbial community at the continental scale, which significantly increased the relative abundance of Proteobacteria and Ascomycota, but decreased Chloroflexi and Basidiomycota. The variations in microbial phyla could be attributed to distinct responses to altered environmental factors after human modifications. This study provides insights into the biogeography of soil microbiota, valuable for regional soil biodiversity assessments and monitoring microbial responses to global changes.

Depth effects on bacterial community altitudinal patterns and assembly processes in the warm-temperate montane forests of China

Soil bacterial communities are essential for ecosystem function, yet their response along altitudinal gradients in different soil strata remains unclear. Understanding bacterial community co-occurrence networks and assembly patterns in mountain ecosystems is crucial for comprehending microbial ecosystem functions. We utilized Illumina MiSeq sequencing to study bacterial diversity and assembly patterns of surface and subsurface soils across a range of elevations (700 to 2100 m) on Dongling Mountain. Our results showed significant altitudinal distribution patterns concerning bacterial diversity and structure in the surface soil. The bacterial diversity exhibited a consistent decrease, while specific taxa demonstrated unique patterns along the altitudinal gradient. However, no altitudinal dependence was observed for bacterial diversity and community structure in the subsurface soil. Additionally, a shift in bacterial ecological groups is evident with changing soil depth. Copiotrophic taxa thrive in surface soils characterized by higher carbon and nutrient content, while oligotrophic taxa dominate in subsurface soils with more limited resources. Bacterial community characteristics exhibited strong correlations with soil organic carbon in both soil layers, followed by pH in the surface soil and soil moisture in the subsurface soil. With increasing depth, there is an observable increase in taxa-taxa interaction complexity and network structure within bacterial communities. The surface soil exhibits greater sensitivity to environmental perturbations, leading to increased modularity and an abundance of positive relationships in its community networks compared to the subsurface soil. Furthermore, the bacterial community at different depths was influenced by combining deterministic and stochastic processes, with stochasticity (homogenizing dispersal and undominated) decreasing and determinism (heterogeneous selection) increasing with soil depth.

Distillers' grains organic fertilizer alters soil bacterial composition and co-occurrence patterns in a tobacco-growing field

In recent years, numerous studies have indicated that the combination of organic and inorganic fertilizers can effectively improve soil fertility and soil productivity. Distillers' grain (DG), the primary by-product of Chinese spirits production, has a high utilization value for producing organic fertilizer. We investigated the effects of distillers' grain organic fertilizer (DGOF) on soil chemical properties and microbial community composition, as well as the effects of chemical properties on the abundance of keystone species. The results indicated that the application of DGOF significantly increased tobacco yield by 14.8% and mainly affected the composition rather than the alpha diversity of the bacterial community. Ten amplicon sequence variants (ASVs) were identified as keystone species in the bacterial communities, and most of their relative abundance was influenced by the DGOF addition through affecting soil chemical properties. Our results elucidated the alterations in soil chemical properties and microbial community composition resulting from DGOF application, which is of great importance to better understand the relationship between DGOF and soil microorganisms in the flue-cured tobacco cultivation field.

Monotonic trends of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China

To investigate microbial communities and their contributions to carbon and nutrient cycling along water gradients can enhance our comprehension of climate change impacts on ecosystem services. Thus, we conducted an assessment of microbial communities, metagenomic functions, and metabolomic profiles within four ecosystems, i.e., desert grassland (DG), shrub-steppe (SS), forest (FO), and marsh (MA) in the Altai region of Xinjiang, China. Our results showed that soil total carbon (TC), total nitrogen, NH4+, and NO3- increased, but pH decreased with soil water gradients. Microbial abundances and richness also increased with soil moisture except the abundances of fungi and protists being lowest in MA. A shift in microbial community composition is evident along the soil moisture gradient, with Proteobacteria, Basidiomycota, and Evosea proliferating but a decline in Actinobacteria and Cercozoa. The β-diversity of microbiomes, metagenomic, and metabolomic functioning were correlated with soil moisture gradients and have significant associations with specific soil factors of TC, NH4+, and pH. Metagenomic functions associated with carbohydrate and DNA metabolisms, as well as phages, prophages, TE, plasmids functions diminished with moisture, whereas the genes involved in nitrogen and potassium metabolism, along with certain biological interactions and environmental information processing functions, demonstrated an augmentation. Additionally, MA harbored the most abundant metabolomics dominated by lipids and lipid-like molecules and organic oxygen compounds, except certain metabolites showing decline trends along water gradients, such as N'-Hydroxymethylnorcotinine and 5-Hydroxyenterolactone. Thus, our study suggests that future ecosystem succession facilitated by changes in rainfall patterns will significantly alter soil microbial taxa, functional potential, and metabolite fractions.

Nutrient structure dynamics and microbial communities at the water-sediment interface in an extremely acidic lake in northern Patagonia

Lake Caviahue (37° 50 'S and 71° 06' W; Patagonia, Argentina) is an extreme case of a glacial, naturally acidic, aquatic environment (pH ~ 3). Knowledge of the bacterial communities in the water column of this lake, is incipient, with a basal quantification of the bacterioplankton abundance distribution in the North and South Basins of Lake Caviahue, and the described the presence of sulfur and iron oxidizing bacteria in the lake sediments. The role that bacterioplankton plays in nutrient utilization and recycling in this environment, especially in the phosphorus cycle, has not been studied. In this work, we explore this aspect in further depth by assessing the diversity of pelagic, littoral and sediment bacteria, using state of the art molecular methods and identifying the differences and commonalties in the composition of the cognate communities. Also, we investigate the interactions between the sediments of Lake Caviahue and the microbial communities present in both sediments, pore water and the water column, to comprehend the ecological relationships driving nutrient structure and fluxes, with a special focus on carbon, nitrogen, and phosphorus. Two major environmental patterns were observed: (a) one distinguishing the surface water samples due to temperature, Fe2+, and electrical conductivity, and (b) another distinguishing winter and summer samples due to the high pH and increasing concentrations of N-NH4+, DOC and SO42-, from autumn and spring samples with high soluble reactive phosphorus (SRP) and iron concentrations. The largest bacterial abundance was found in autumn, alongside higher levels of dissolved phosphorus, iron forms, and increased conductivity. The highest values of bacterial biomass were found in the bottom strata of the lake, which is also where the greatest diversity in microbial communities was found. The experiments using continuous flow column microcosms showed that microbial growth over time, in both the test and control columns, was accompanied by a decrease in the concentration of dissolved nutrients (SRP and N-NH4+), providing proof that sediment microorganisms are active and contribute significantly to nutrient utilization/mobilization.

Prolonged water limitation shifts the soil microbiome from copiotrophic to oligotrophic lifestyles in Scots pine mesocosms

Reductions in soil moisture due to prolonged episodes of drought can potentially affect whole forest ecosystems, including soil microorganisms and their functions. We investigated how the composition of soil microbial communities is affected by prolonged episodes of water limitation. In a mesocosm experiment with Scots pine saplings and natural forest soil maintained at different levels of soil water content over 2 years, we assessed shifts in prokaryotic and fungal communities and related these to changes in plant development and soil properties. Prolonged water limitation induced progressive changes in soil microbial community composition. The dissimilarity between prokaryotic communities at different levels of water limitation increased over time regardless of the recurrent seasons, while fungal communities were less affected by prolonged water limitation. Under low soil water contents, desiccation-tolerant groups outcompeted less adapted, and the lifestyle of prokaryotic taxa shifted from copiotrophic to oligotrophic. While the abundance of saprotrophic and ligninolytic groups increased alongside an accumulation of dead plant material, the abundance of symbiotic and nutrient-cycling taxa decreased, likely impairing the development of the trees. Overall, prolonged episodes of drought appeared to continuously alter the structure of microbial communities, pointing to a potential loss of critical functions provided by the soil microbiome.

Replacing traditional pretreatment in one-step UF with natural short-distance riverbank filtration: Continuous contaminants removal and TMP increase relief

Scientists have been focusing on applying more natural processes instead of industrial chemicals in drinking water treatment to achieve the purpose of carbon emissions reduction. In this study, we shortened the infiltration range of riverbank filtration, a natural water purification process, to form the short-distance riverbank filtration (sRBF) which retained its ability in water quality improvement and barely influenced the groundwater environment, and integrated it with ultrafiltration (UF) to form a one-step sRBF-UF system. This naturalness-artificiality combination could realize stable contaminants removal and trans-membrane pressure (TMP) increase relief for over 30 days without dosing chemicals. Generally, both sRBF and UF played the important role in river water purification, and the interaction between them made the one-step sRBF-UF superior in long-term operation. The sRBF could efficiently remove contaminants (90 % turbidity, 60 % total nitrogen, 30 % ammonia nitrogen, and 25 % total organic carbon) and reduce the membrane fouling potential of river water under its optimum operation conditions, i.e., a hydraulic retention time of 48 h, an operation temperature of 20 °C, and a synergistic filter material of aquifer and riverbank soil. Synergistic adsorption, interception, and microbial biodegradation were proved to be the mechanisms of contaminants and foulants removal for sRBF. The sequential UF also participated in the reduction of impurities and especially played a role in intercepting microbial metabolism products and possibly leaked microorganisms from sRBF, assuring the safety of product water. To date, the one-step sRBF-UF was a new attempt to combine a natural process with an artificial one, and realized a good and stable product quality in long-term operation without doing industrial chemicals, which made it a promised alternative for water purification for cities alongside the river.

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

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

Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs

BACKGROUND

Frogs are critical economic animals essential to agricultural ecosystem equilibrium. However, Meningitis-like Infectious Disease (MID) often affects them in agricultural settings. While frog-associated microbiota contribute to elemental cycling and immunity, the effects of frog sex and health on gut bacteria remain understudied, and the relationship between frog habitat and soil microbes is unclear. We aimed to determine how frog sex, health status and habitat influence symbiotic bacteria and community assembly mechanism to provide guidance for sustainable frog farming and conservation.

RESULTS

We employed 16S rRNA sequencing to investigate gut microbiota differences in relation to frog sex and health status. We also compared symbiotic communities in frog-aggregation, native and soybean soil on the farm. Results showed that gut bacterial β-diversity and taxonomy were markedly influenced by frog sex and health. Healthy frogs had more robust gut bacterial metabolism than frogs infected with MID. Cooccurrence network analysis revealed that healthy female frogs had more complex microbial network structure than males; however, diseased males showed the greatest network complexity. The assembly mechanism of gut bacteria in male frogs was dominated by deterministic processes, whereas in female frogs it was dominated by stochastic processes. Among symbiotic bacteria in frog habitat soils, deterministic processes predominantly shaped the community assembly of soybean soil. In particular, soybean soil was enriched in pathogens and nitrogen functions, whereas frog-aggregation soil was markedly increased in sulphur respiration and hydrocarbon degradation.

CONCLUSION

Our study reveals that sex mainly alters the interaction network and assembly mechanism of frog intestinal bacteria; MID infection significantly inhibits the metabolic functions of intestinal bacteria. Furthermore, diverse frog habitat soils could shape more symbiotic bacteria to benefit frog farming. Our findings provide new horizons for symbiotic bacteria among frogs, which could contribute to sustainable agriculture and ecological balance.

Soil protists are more resilient to the combined effect of microplastics and heavy metals than bacterial communities

Heavy metals and micro-/nanoplastic pollution seriously threaten the environment and ecosystems. While many studies investigated their effects on diverse microbes, few studies have focused on soil protists, and it is unclear how soil protists respond to the combined effect of micro-/nanoplastics and heavy metals. This study investigated how soil protistan and bacterial communities respond to single or combined copper and micro-/nanoplastics. The bacterial community exhibited an instantaneous response to single copper pollution, whereas the combined pollution resulted in a hysteresis effect on the protistan community. Single and combined pollution inhibited the predation of protists and changed the construction of ecological networks. Though single and combined pollution did not significantly affect the overall community structure, the exposure experiment indicated that combined pollution harmed soil amoeba's fitness. These findings offer valuable new insights into the toxic effects of single and combined pollution of copper and plastics on soil protistan and bacterial communities. Additionally, this study shows that sequencing-based analyses cannot fully reflect pollutants' adverse effects, and both culture-independent and dependent methods are needed to reveal the impact of pollutants on soil microbes.

Phytoremediation with application of anaerobic fermentation residues regulate the assembly of ecological clusters within co-occurrence network in ionic rare earth tailings soil: A pot experiment

The cultivation of energy plants (Pennisetum hybrid) with anaerobic fermentation residues has become an important phytoremediation approach in ionic rare earth elements (REEs) tailings because of its advantages in low cost and sustainability recently. In this study, a comparative pot experiment was carried out to determine the interaction pattern and key ecological clusters in microbial community respond to phytoremediation. Results showed that the application of biogas residues or slurry could effectively mitigate soil acidification, increase soil nutrients, alter REEs bioavailability and promote plant growth. Without fertilization, plant growth was restricted and soil acidification and nutrient-deficiency would be further aggravated. This difference in phytoremediation effect was associated with the assembly of seven key ecological clusters in co-occurrence network of rhizosphere soil. And such assembly pattern of cluster, determined by the environmental preference (e.g. pH, REEs), nutrient demand and interaction among clusters, could alter the microbial communities in response to the changes in soil context rapidly and exert corresponding ecological function during phytoremediation, such as participating in soil nutrient cycling, affecting plant biomass and altering REEs bioavailability. These findings provided new insights for anaerobic fermentation residues application, and can be beneficial to support for studying microbe-plant combined remediation in the future.

Breaking the Ice: A Review of Phages in Polar Ecosystems

Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.

Soil Microbiome in Conditions of Oil Pollution of Subarctic Ecosystems

The present study aimed to investigate the recovery of soil quality and the bacterial and fungal communities following various recultivation methods in areas contaminated with oil. Oil spills are known to have severe impacts on ecosystems; thus, the restoration of contaminated soils has become a significant challenge nowadays. The study was conducted in the forest-tundra zone of the European North-East, where 39 soil samples from five oil-contaminated sites and reference sites were subjected to metagenomic analyses. The contaminated sites were treated with different biopreparations, and the recovery of soil quality and microbial communities were analyzed. The analysis of bacteria and fungi communities was carried out using 16S rDNA and ITS metabarcoding. It was found that 68% of bacterial OTUs and 64% of fungal OTUs were unique to the reference plot and not registered in any of the recultivated plots. However, the species diversity of recultivated sites was similar, with 50-80% of bacterial OTUs and 44-60% of fungal OTUs being common to all sites. New data obtained through soil metabarcoding confirm our earlier conclusions about the effectiveness of using biopreparations with indigenous oil-oxidizing micro-organisms also with mineral fertilizers, and herbaceous plant seeds for soil remediation. It is possible that the characteristics of microbial communities will be informative in the bioindication of soils reclaimed after oil pollution.

Bacterial diversity of biofilms on polyhydroxybutyrate exposed to marine conditions: Ex-situ vs. in-situ tests

Biofilms form on any available surface and, depending on the characteristics of the material and the environmental conditions, biodegradation can take place. We compared the bacterial composition of polyhydroxybutyrate (PHB)-related biofilm communities from marine ex-situ and in-situ tests to assess the differences in diversity and abundance between these two biofilms. This comparison will help to better assess the transferability of tank tests to real-life scenarios. The in-situ tests were set up in the Mediterranean Sea on the Island of Elba, Italy where PHB-tensile bars were lodged in the sediments. This created a water-exposed aerobic and mud-planted anaerobic scenario. The ex-situ tests were modeled after in-situ tests and performed in temperature-controlled tanks. The PHB-related biofilms were harvested after 240 days of exposure along with planktonic bacteria, and particle- and sediment-related biofilm. The bacterial composition was elucidated using 16S rDNA sequencing. Biofilms harvested from the in-situ test were more diverse, less even, and contained more rare species compared to biofilms from the ex-situ test. The PHB-related biofilm was characterized by a higher abundance of the bacterial order Desulfobacterales. The composition of PHB-related biofilm varied significantly between the two tests and between aerobic and anaerobic conditions. The composition of PHB-related biofilm was significantly different from planktonic bacteria, particle, and sediment-related biofilm, showing the influence of PHB on the biofilm composition. Thus, the ex-situ tank test for PHB degradation cannot, in terms of bacterial composition, simulate the in-situ conditions to their full extent.

Reveal molecular mechanism on the effects of silver nanoparticles on nitrogen transformation and related functional microorganisms in an agricultural soil

Silver nanoparticles (AgNPs) are widely present in aquatic and soil environment, raising significant concerns about their impacts on creatures in ecosystem. While the toxicity of AgNPs on microorganisms has been reported, their effects on biogeochemical processes and specific functional microorganisms remain relatively unexplored. In this study, a 28-day microcosmic experiment was conducted to investigate the dose-dependent effects of AgNPs (10 mg and 100 mg Ag kg-1 soil) on nitrogen transformation and functional microorganisms in agricultural soils. The molecular mechanisms were uncovered by examining change in functional microorganisms and metabolic pathways. To enable comparison, the toxicity of positive control with an equivalent Ag+ dose from CH3COOAg was also included. The results indicated that both AgNPs and CH3COOAg enhanced nitrogen fixation and nitrification, corresponding to increased relative abundances of associated functional genes. However, they inhibited denitrification via downregulating nirS, nirK, and nosZ genes as well as reducing nitrate and nitrite reductase activities. In contrast to high dose of AgNPs, low levels increased bacterial diversity. AgNPs and CH3COOAg altered the activities of associated metabolic pathways, resulting in the enrichment of specific taxa that demonstrated tolerance to Ag. At genus level, AgNPs increased the relative abundances of nitrogen-fixing Microvirga and Bacillus by 0.02 %-629.39 % and 14.44 %-30.10 %, respectively, compared with control group (CK). The abundances of denitrifying bacteria, such as Rhodoplanes, Pseudomonas, and Micromonospora, decreased by 19.03 % to 32.55 %, 24.73 % to 50.05 %, and 15.66 % to 76.06 %, respectively, compared to CK. CH3COOAg reduced bacterial network complexity, diminished the symbiosis mode compared to AgNPs. The prediction of genes involved in metabolic pathways related to membrane transporter and cell motility showed sensitive to AgNPs exposure in the soil. Further studies involving metabolomics are necessary to reveal the essential effects of AgNPs and CH3COOAg on biogeochemical cycle of elements in agricultural soil.

Biodegradation of microplastic in freshwaters: A long-lasting process affected by the lake microbiome

Plastics have been produced for over a century, but definitive evidence of complete plastic biodegradation in different habitats, particularly freshwater ecosystems, is still missing. Using 13 C-labelled polyethylene microplastics (PE-MP) and stable isotope analysis of produced gas and microbial membrane lipids, we determined the biodegradation rate and fate of carbon in PE-MP in different freshwater types. The biodegradation rate in the humic-lake waters was much higher (0.45% ± 0.21% per year) than in the clear-lake waters (0.07% ± 0.06% per year) or the artificial freshwater medium (0.02% ± 0.02% per year). Complete biodegradation of PE-MP was calculated to last 100-200 years in humic-lake waters, 300-4000 years in clear-lake waters, and 2000-20,000 years in the artificial freshwater medium. The concentration of 18:1ω7, characteristic phospholipid fatty acid in Alpha- and Gammaproteobacteria, was a predictor of faster biodegradation of PE. Uncultured Acetobacteraceae and Comamonadaceae among Alpha- and Gammaproteobacteria, respectively, were major bacteria related to the biodegradation of PE-MP. Overall, it appears that microorganisms in humic lakes with naturally occurring refractory polymers are more adept at decomposing PE than those in other waters.

Selection of aquatic microbiota exposed to the herbicides flufenacet and metazachlor

Herbicides are important, ubiquitous environmental contaminants, but little is known about their interaction with bacterial aquatic communities. Here, we sampled a protected natural freshwater habitat and characterised its microbiome in interaction with herbicides. We evolved the freshwater microbiomes in a microcosm assay of exposure (28 days) to flufenacet and metazachlor at environmental concentrations of 0.5, 5 and 50 μg L-1 . Inhibitory effects of herbicides were exemplarily assessed in cultured bacteria from the same pond (Pseudomonas alcaligenes, Paenibacillus amylolyticus and Microbacterium hominis). Findings were compared to long-term concentrations as provided by local authorities. Here, environmental concentrations reached up to 11 μg L-1 (flufenacet) and 76 μg L-1 (metazachlor). Bacteria were inhibited at minimum inhibitory concentrations far above these values; however, concentrations of 50 μg L-1 of flufenacet resulted in measurable growth impairment. While most herbicide-exposed microcosm assays did not differ from controls, Acidobacteria were selected at high environmental concentrations of herbicides. Alpha-diversity (e.g., taxonomic richness on phylum level) was reduced when aquatic microbiomes were exposed to 50 μg metazachlor or flufenacet. One environmental strain of P. alcaligenes showed resistance to high concentrations of flufenacet (50 g L-1 ). In total, this study reveals that ecologic imbalance due to herbicide use significantly impacts aquatic microbiomes.

Enhancing nutrient recovery from food waste anaerobic digestate

The study synthesised the raw liquid fraction of digestate into a nutrient rich solid digestate through acidification whilst preventing nitrogen loss through ammonium volatilisation during evaporation. To stabilise ammonium in the digestate, it was acidified with sulphuric, nitric, and phosphoric acid to produce solid digestate with ammonium sulphate, ammonium nitrate and ammonium phosphate, respectively. These treatments were compared against urea ammonium nitrate, raw digestate, and unacidified solid digestate. To evaluate the effect of these transformed digestate products in soil, a plant growth experiment (Kikuyu; Cenchrus clandestinus) was conducted, and characterised, plant growth, soil chemistry, and rhizosphere bacterial communities. Plant growth was enhanced by all digestate treatments compared to control and urea ammonium nitrate. Ammonium phosphate solid digestate plant growth was significantly higher than all other acidified treatments due to the high P content. Moreover, digestate-amended soil had elevated Proteobacteria and putative denitrification genes.

Prokaryotic communities inhabiting a high-radon subterranean ecosystem (Castañar Cave, Spain): Environmental and substrate-driven controls

Castañar Cave (Caceres, Spain) is a unique show cave known for its high natural radiation levels. This study presents a comprehensive analysis of its prokaryotic diversity, specifically focusing on investigating the influence of environmental conditions and substrate characteristics on the prokaryotic community structure in the cave sediments. Additionally, the research aims to evaluate the potential impact of human activities on the cave ecosystem. The identification of distinct bioclimatic zones within the cave was made possible through a combination of environmental and microbial monitoring (ATP assays). The results reveal sediment texture as a significant factor, notably affecting the structure, diversity, and phylogenetic variability of the microbial community, including both Bacteria and Archaea. The proportion of clay minerals in sediments plays a crucial role in regulating moisture levels and nutrient availability. These substrate properties collectively exert a significant selective pressure on the structure of prokaryotic communities within cave sediments. The molecular approach shows that heterotrophic bacteria, including those with chitinolytic enzymes, primarily inhabit the cave. Furthermore, chemoautotrophic nitrifiers such as the archaea Nitrososphaeria and the genus Nitrospira, as well as methanotrophic bacteria from the phyla Methylomirabilota, Pseudomonadota, and Verrucomicrobiota, are also present. Remarkably, despite being a show cave, the cave microbiota displays minimal impacts from human activities and the surface ecosystem. Prokaryotic populations exhibit stability in the innermost areas, while the tourist trail area experiences slightly higher biomass increases due to visitor traffic. This suggests that conservation efforts have successfully limited the entry of external nutrients into the innermost cave areas. Additionally, the results suggest that integrating biomarkers like ATP into environmental monitoring can significantly enhance the methods used to study the negative impacts of tourism on cave ecosystems.

Australian soil microbiome: A first sightseeing regional prediction driven by cycles of soil temperature and pedogenic variations

Declines in soil multifunctionality (e.gsoil capacity to provide food and energy) are closely related to changes in the soil microbiome (e.g., diversity) Determining ecological drivers promoting such microbiome changes is critical knowledge for protecting soil functions. However, soil-microbe interactions are highly variable within environmental gradients and may not be consistent across studies. Here we propose that analysis of community dissimilarity (β-diversity) is a valuable tool for overviewing soil microbiome spatiotemporal changes. Indeed, β-diversity studies at larger scales (modelling and mapping) simplify complex multivariate interactions and refine our understanding of ecological drivers by also giving the possibility of expanding the environmental scenarios. This study represents the first spatial investigation of β-diversity in the soil microbiome of New South Wales (800,642 km2 ), Australia. We used metabarcoding soil data (16S rRNA and ITS genes) as exact sequence variants (ASVs) and UMAP (Uniform Manifold Approximation and Projection) as the distance metric. β-Diversity maps (1000-m resolution)-concordance correlations of 0.91-0.96 and 0.91-0.95 for bacteria and fungi, respectively-showed soil biome dissimilarities driven primarily by soil chemistry-pH and effective cation exchange capacity (ECEC)-and cycles of soil temperature-land surface temperature (LST-phase and LST-amplitude). Regionally, the spatial patterns of microbes parallel the distribution of soil classes (e.g., Vertosols) beyond spatial distances and rainfall, for example. Soil classes can be valuable discriminants for monitoring approaches, for example pedogenons and pedophenons. Ultimately, cultivated soils exhibited lower richness due to declines in rare microbes which might compromise soil functions over time.