Microbial Community Activity Research Articles

Stochastic Processes Dominate the Assembly of Soil Bacterial Communities of Land Use Patterns in Lesser Khingan Mountains, Northeast China

To meet the demands of a growing population, natural wetlands are being converted to arable land, significantly impacting soil biodiversity. This study investigated the effects of land use changes on bacterial communities in wetland, arable land, and forest soils in the Lesser Khingan Mountains using Illumina MiSeq 16S rRNA sequencing. Soil physicochemical properties and enzyme activities were measured using standard methods, while microbial diversity was assessed through sequencing analysis. Our findings revealed that forest soils had significantly higher levels of total potassium (2.62 g·kg−1), electrical conductivity (8.22 mS·cm−1), urease (0.18 mg·g−1·d−1), and nitrate reductase (0.13 mg·g−1·d−1), attributed to rich organic matter and active microbial communities. Conversely, arable soils showed lower total potassium (1.94 g·kg−1), reduced electrical conductivity, and suppressed enzyme activities due to frequent tilling and fertilization. Wetland soils exhibited the lowest values primarily due to water saturation, which limits organic matter decomposition and microbial activity. Land use changes notably reduced microbial diversity, with conversion from forest to arable land leading to habitat loss. Forest soils supported higher abundances of Proteobacteria (37.59%) and Actinobacteriota (34.73%), while arable soils favored nitrogen-fixing bacteria. Wetlands were characterized by chemoheterotrophic and anaerobic bacteria. Overall, these findings underscore the profound influence of land use on soil microbial communities and their functional roles, highlighting the need for sustainable management practices.

Application of a metatranscriptomics technology, CSI-Dx, for the detection of pathogens associated with prosthetic joint infections

Preoperative identification of causal organism(s) is crucial for effective prosthetic joint infection treatment. Herein, we explore the clinical application of a novel metatranscriptomic (MT) workflow, CSI-Dx, to detect pathogens associated with prosthetic joint infection. MT provides insight into transcriptionally active microbes, overcoming limitations of culture-based and available molecular methods. This study included 340 human synovial fluid specimens subjected to CSI-Dx and traditional culture-based methods. Exploratory analyses were conducted to determine sensitivity and specificity of CSI-Dx for detecting clinically-relevant taxa. Our findings provide insights into the active microbial community composition of synovial fluid from arthroplasty patients and demonstrate the potential clinical utility of CSI-Dx for aiding prosthetic joint infection diagnosis. This approach offers potential for improved sensitivity and acceptable specificity compared to synovial fluid culture, enabling detection of culturable and non-culturable microorganisms. Furthermore, CSI-Dx provides valuable information on antimicrobial resistance gene expression. While further optimization is needed, integrating metatranscriptomic technologies like CSI-Dx into routine clinical practice can revolutionize prosthetic joint infection diagnosis by offering a comprehensive and active snapshot of associated pathogens.

Microbiological and chemical corrosion study of Egyptian petroleum samples: microbial community and corrosion activity

Microbiological and chemical corrosion study of Egyptian petroleum samples: microbial community and corrosion activity

Warming increases CH4 emissions from rice paddies through shifts in methanogenic and methanotrophic communities

Warming often stimulates methane (CH4) emissions from rice paddies, one of the largest anthropogenic sources of CH4 emissions. However, the responses of methanogenic and methanotrophic communities to warming, particularly within active communities, remain unclear. Therefore, based on a field warming experiment in a rice-wheat system, we investigated the effects of warming on methanogenic and methanotrophic communities, using the DNA stable-isotope probing technology. Our results indicated that warming increased CH4 emissions by 27–49% over two rice growing seasons compared to ambient conditions. Warming significantly increased the abundance of methanogens by 53%, whereas did not affect activities of methanogens and active methanogenic community. Conversely, warming did not influence the abundance of methanotrophs, but reduced activities of methanotrophs by 44%. Notably, warming led to a significant rise in the relative abundance of the active type II methanotrophic community, which exhibits lower CH4 oxidation efficiency. These findings suggest that the observed increase in CH4 emissions under warming conditions is primarily driven by the enhanced abundance of methanogens and the increased presence of less efficient active type II methanotrophs. This study underscores the critical role of active microbial communities in understanding and managing CH4 emissions from rice paddies in a warming world.

Perennial crops shape the soil microbial community and increase the soil carbon in the upper soil layer

Soil biodiversity is threatened by intensive agriculture that relies on annual grain crop production, thus leading to a decline in soil functions and ecosystem services. Perennial grain crops have a positive impact on the soil microbial community, but the responsive microbial groups and the magnitude of their response remain uncertain. To elucidate this, we analysed soil microbial biomass and community composition, bacterial growth and soil total carbon in five crops: organic perennial intermediate wheatgrass (IWG, Thinopyrum intermedium, Kernza®), organic IWG-alfalfa intercrop, organic biennial grass-legume mixture, organic annual wheat or rye and conventional annual wheat. The analysis was carried out at three time points under two growing seasons at four different soil depths. Five years after establishment, IWG had greater amounts of soil total fungi and bacteria, and of arbuscular mycorrhizal (AM) fungi, saprotrophic fungi, gram-negative (G−) and gram-positive (G+) bacteria compared to annual wheat. Crop perenniality influenced the soil microbial community structure although precipitation, soil temperature and water content were the main drivers of the patterns of and temporal variations in the microbial community. Perennial crops, with reduced tillage and low nitrogen input management increased the proportions of fungi relative to bacteria, AM fungi to saprotrophic fungi, G− bacteria to G+ bacteria, and the growth rate of total bacteria. This resulted in a more active soil microbial community with higher microbial biomass than annual wheat and contributed to the increased soil total carbon storage in the 0–5 cm soil layer in a humid continental climate. The findings emphasize the importance of combining a no tillage strategy with long-term vegetation cover to increase soil quality.

Ultrafast metaproteomics for quantitative assessment of strain isolates and microbiomes

BackgroundMicrobial communities are essential in human health and environmental regulation, but present a challenge for the analytical science due to their diversity and dynamic range. Tandem mass spectrometry provides functional insights on microbial life cycle, but is time-consuming. MALDI TOF excels in rapid species identification, but not functional assessment. To address critical challenges in human health and environmental sustainability, microbiology needs advanced mass spectrometry methods and bioinformatic tools enabling both rapid identification and accurate assessment of functional activity of microbial communities. ResultsWe show for the first time that both identity and functional activity of microorganisms and their communities can be accurately determined in experiments as short as 7 min per sample, using the basic Orbitrap MS configuration without peptide fragmentation. The approach was validated using strain isolates, mock microbiomes composed of bacteria spiked at known concentrations and human fecal microbiomes. Our new bioinformatic algorithm identifies the bacterial species with an accuracy of 95 %, when no prior information on the sample is available. Microbiome composition was resolved at the genus level with the mean difference between the actual and identified components of 12 %. For mock microbiomes, Pearson coefficient of up to 0.97 was achieved in estimates of strain biomass change. By the example of Rhodococcus biodegradation of n-alkanes, phenols and its derivatives, we showed the accurate assessment of functional activity of strain isolates, compared with the standard label-free and label-based approaches. SignificanceOur approach makes microbial proteomics fast, functional and insightful using the Orbitrap instruments even without employing peptide fragmentation technology. The approach can be applied to any microorganisms and can take a niche in routine functional assessment of microbial pathogens and consortiums in clinical diagnostics together with MALDI TOF MS and 16S rRNA gene sequencing.

Modulating phytoremediation: How drip irrigation system affect performance of active green wall and microbial community changes

A recent innovation in air phytoremediation is active green walls, which utilises biofiltration technology with airflow from mechanical ventilation. While this novel technology is gaining traction, the influence of irrigation on soil moisture, and subsequently the microbial communities that play a role in air filtration is untested. In this study, the application of drip irrigation techniques in active green walls were investigated for their influence on system performance. A modular green wall system was tested, with tests across 7 different plant species, as well as a substrate only control. Water distribution across the modules, the water-carrying capacity and airflow through the substrate were measured. The microbial community present, which is critical to the phytoremediation process, was quantified by identifying individual microbial phospholipid fatty acids (PLFA) within the substrate. Results demonstrated that the lower-speed drip irrigation reduced water consumption compared to the rapid system, and had generally more uniform moisture distribution. High flow drip irrigation resulted in a water pathway phenomenon, leading to uneven moisture distribution within the green wall, and this effect was accentuated with fibrous root plant species. Drip irrigation did not change microbial community composition across planted modules, apart from increasing fungi by 6%, but did wash out bacteria at the high flow rate used (−56.67%), thus low flow rate irrigation rate is more beneficial for both plant growth and microbial community composition. The current work provides evidence that drip irrigation has considerable effects on both substrate airflow rate and substrate microbial density: both key to system air cleaning performance.

Deciphering the active bacteria involving glucose-triggered priming effect in soils with gradient N inputs

The soil priming effect, which refers to the alteration of soil organic matter (SOM) decomposition due to labile carbon (C) inputs, is widely acknowledged for its impact on C storage in terrestrial ecosystems. However, the impact of chronic nitrogen (N) fertilizer on soil priming effect, particularly in agroecological systems, remains unclear. Here, we utilized soils subjected to varying levels of N fertilization (0, 140, 280, 470, and 660 kg N ha−1 y−1), which were collected from a long-term experimental site. Enzyme activity related to C, N, and phosphorus (P) acquisition was measured using the fluorometric method. Additionally, DNA-based stable isotope probing with 13C-labeled glucose was conducted to explore the role of active bacterial communities (16S rRNA gene analysis) on the priming effect in soils with different N fertilization histories. Glucose addition enhanced the decomposition of native SOM and induced positive priming effects in all soils, which were amplified by the historical N application level. Activity of C-related enzymes essential for soil C decomposition increased following glucose addition, which was positively correlated with the soil priming effect. Active bacterial taxa, primarily Firmicutes, Actinobacteria, and Proteobacteria, were capable of assimilating exogenous glucose-C or native SOM-C. Notably, bacteria assimilating glucose exhibited higher abundance-weighted average ribosomal RNA gene operon copy number than those assimilating SOM, indicating the role of r-strategists in accelerating SOC turnover and increasing C loss. These findings highlight the role of active microbial community attributes on the soil priming effects. This study provides new insights into the intricate processes of C transformation in soils subjected to long-term N management in agroecosystems.

Biodegradation of thermoplastic starch by a newly isolated active microbial community: Deciphering the biochemical mechanisms controlling bioprocess robustness

Defining sustainable end-of-life routes for bioplastics comprises a task of outmost importance, while biological recycling constitutes the most favorable option for several biopolymers, such as thermoplastic starch (TPS). To our knowledge, this is the first study to assess the biodegradation of TPS pellets and films in aqueous cultures employing an acclimated microbial community. Biological treatment of bioplastics displayed a two-phase pattern that included different biodegradation rates, where TPS removal in the first phase remained high and decelerated in the second phase reaching a plateau. Thus, TPS weight reduction of 14.8 % was observed using pellets following 10 d of incubation, while although films exhibited higher reduction (slightly over 30 % in 15 d), the biodegradation rate was significantly reduced thereafter. Several changes of starch related bands were detected (using FTIR) in the surface of both pellets and films during the bioprocess, indicating induction of a common biodegradation pathway. Distinct bacterial assemblages were formed during the TPS biodegradation process and statistically significant differences were detected in the abundance of several genera between the two degradation phases. Fungal communities were more stable (Fusarium and Neocosmospora were dominant at all times) and there was no effect of biofilm or degradation phase on fungal community composition. Overall, a more diverse community incorporating lower catalytic activity was gradually formed, as confirmed by the shift between k-stategist and r-stategist taxa monitored, while crystalline over amorphous regions were enhanced in the biopolymer during TPS biodegradation, responses consistent with the biodegradation rate reduction observed in the plateau stage. The study highlighted the biochemical mechanism limiting TPS biodegradation processes and the significant potential of the newly isolated community in the development of TPS waste treatment technologies.

Transcriptional profiling elucidates biofilm functionality in the dynamic environment of an enhanced biological phosphorus removal reactor

ABSTRACT Recently, biofilms, complex and dynamic structures of microorganisms, have been applied to enhanced biological phosphorus removal (EBPR), a wastewater treatment configuration dependent on cyclic shifts between anaerobic and aerobic conditions. In this study, comparative metagenomics and metatranscriptomics were performed on biofilms collected from seven sites of a moving-bed-biofilm-reactor-based EBPR process. The aim was to examine the functional ecology of phosphorus-accumulating biofilms throughout a single EBPR cycle. Taxonomic profiling revealed high microbial diversity, stable throughout the EBPR cycle. The dominant phosphorus-accumulating organisms (PAOs) were identified as Candidatus accumulibacter, Candidatus phosphoribacter, and Candidatus lutibacillus. However, these did not show the highest transcriptional activities. Propionivibrio, a potential glycogen-accumulating organism, was the most transcriptionally active. Comparative analysis of biofilms from different EBPR stages showed a progressive change in metatranscriptome composition, correlating with nutrient removal. Analysis of differentially expressed genes in abundant PAOs revealed key genes associated with the uptake of phosphorus, degradation of glycogen, biosynthesis of polyhydroxyalkanoates, and acetate production. In conclusion, this study reveals that biofilms possess the capability to adapt to environmental fluctuations primarily through alterations in microbial gene expression activity and subsequent metabolic modulation, and dominant taxa may not necessarily exhibit the highest transcriptional activity in complex microbial communities.

Individual methanogenic granules are whole-ecosystem replicates with reproducible responses to environmental cues

BackgroundIn this study, individual methanogenic (anaerobic), granular biofilms were used as true community replicates to assess whole-microbial-community responses to environmental cues. The aggregates were sourced from a lab-scale, engineered, biological wastewater treatment system, were size-separated, and the largest granules were individually subjected to controlled environmental cues in micro-batch reactors (μBRs).ResultsIndividual granules were identical with respect to the structure of the active community based on cDNA analysis. Additionally, it was observed that the active microbial community of individual granules, at the depth of 16S rRNA gene sequencing, produced reproducible responses to environmental changes in pH, temperature, substrate, and trace-metal supplementation. We identified resilient and susceptible taxa associated with each environmental condition tested, as well as selected specialists, whose niche preferences span the entire trophic chain required for the complete anaerobic degradation of organic matter.ConclusionsWe found that single anaerobic granules can be considered highly-replicated whole-ecosystems with potential usefulness for the field of microbial ecology. Additionally, they act as the smallest whole-community unit within the meta-community of an engineered bioreactor. When subjected to various environmental cues, anaerobic granules responded reproducibly allowing for rare or unique opportunities for high-throughput studies testing whole-community responses to a wide range of environmental conditions.

Effect of long-term liquid dairy manure application on activity and structure of bacteria and archaea in no-till soils depends on plant in development.

This study aimed to evaluate the impact of long-term liquid dairy manure (LDM) application on the activity and structure of soil bacterial and archaea communities in two cropping seasons over 1year of a no-till crop rotation system. The experiment was run in a sandy clay loam texture Oxisol, in Brazil, including LDM doses of 60, 120, and 180 m3ha-1year-1, installed in 2005. Soil sampling was conducted during spring 2018 and autumn 2019 at 0-10-cm depth. Microbial biomass carbon and nitrogen, 16S rRNA gene sequencing, microbial respiration and quotient were performed. Over the 14-year period, LDM application increased soil microbial community activity. Analysis of 16S rRNA gene sequencing revealed dominance by Proteobacteria, Acidobacteria, and Actinobacteria phyla (67% in spring and 70% in autumn). Genera Pirulla and Nitrososphaera showed enrichment at LDM doses of 120 and 180 m3ha-1year-1 doses, respectively. During spring, following black oat cropping, shifts in the relative abundance of Bacteroidetes, Proteobacteria, Firmicutes, Gemmatimonadetes, Verrucomicrobia, Chloroflexi, Actinobacteria, and AD3 phyla were observed due to LDM application, correlating with soil chemical indicators such as pH, K, Ca, Mn, and Zn. Our findings indicate that plant development strongly influences microbial community composition, potentially outweighing the impact of LDM. Our findings indicate that the application of liquid dairy manure alters the soil bacterial activity and community; however, this effect depends on the developing plant.

Survival of Probiotic Bacterial Cells in the Upper Gastrointestinal Tract and the Effect of the Surviving Population on the Colonic Microbial Community Activity and Composition.

Many health-promoting effects have been attributed to the intake of probiotic cells. However, it is important that probiotic cells arrive at the site of their activity in a viable state in order to exert their beneficial effects. Careful selection of the appropriate probiotic formulation is therefore required as mainly the type of probiotic species/strain and the administration strategy may affect survival of the probiotic cells during the upper gastrointestinal (GIT) passage. Therefore, the current study implemented Simulator of the Human Microbial Ecosystem (SHIME®) technology to investigate the efficacy of different commercially available probiotic formulations on the survival and culturability of probiotic bacteria during upper GIT passage. Moreover, Colon-on-a-Plate (CoaP™) technology was applied to assess the effect of the surviving probiotic bacteria on the gut microbial community (activity and composition) of three human donors. Significantly greater survival and culturability rates were reported for the delayed-release capsule formulation (>50%) as compared to the powder, liquid, and standard capsule formulations (<1%) (p < 0.05), indicating that the delayed-release capsule was most efficacious in delivering live bacteria cells. Indeed, administration of the delayed-release capsule probiotic digest resulted in enhanced production of SCFAs and shifted gut microbial community composition towards beneficial bacterial species. These results thus indicate that careful selection of the appropriate probiotic formulation and administration strategy is crucial to deliver probiotic cells in a viable state at the site of their activity (distal ileum and colon).

Mining metagenomic data to gain a new insight into the gut microbial biosynthetic potential in placental mammals.

Mammals host a remarkable diversity and abundance of gut microbes. Biosynthetic gene clusters (BGCs) in microbial genomes encode biologically active chemical products and play an important role in microbe-host interactions. Traditionally, the exploration of gut microbial metabolic functions has relied on the pure culture method. However, given the limited amounts of microbes being cultivated, insights into the metabolism of gut microbes in mammals continued to be very limited. In this study, we adopted a computational pipeline for mining the metagenomic data (named taxonomy-guided identification of biosynthetic gene clusters, TaxiBGC) to identify experimentally verified BGCs in 373 metagenomes across 53 mammalian species in an unbiased manner. We demonstrated that polyketides (PKs) and nonribosomal peptides (NRPs) are representative of mammals, and the products derived from them were associated with cell-cell communication and resistance to inflammation. Large carnivores had the highest number of BGCs, followed by large herbivores and small mammals. We also observed that the large mammals had more common BGCs that aid in the biosynthesis of a variety of natural products. However, small mammals not only had fewer BGCs but were also unique to each species. Our results provide novel insights into the mining of metagenomic data sets to identify active BGCs and their products across mammals.IMPORTANCEThe gut microbes host numerous biosynthetic gene clusters (BGCs) that biosynthesize natural products and impact the host's physiology. Historically, our understanding of BGCs in mammalian gut microbes was largely based on studies on cultured isolates; however, only a small fraction of mammal-associated microbes have been investigated. The biochemical diversity of the mammalian gut microbiota is poorly understood. Metagenomic sequencing contains data from a vast number of organisms and provides information on the total gene content of communities. Unfortunately, the existing BGC prediction tools are designed for individual microbial genomes. Recently, a BGC prediction tool called the taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC) that directly mine the metagenome was developed. To gain new insights into the microbial metabolism, we used TaxiBGC to predict BGCs from 373 metagenomes across 53 mammalian species representing seven orders. Our findings elucidate the functional activities of complex microbial communities in the gut.

First evidence for temperature’s influence on the enrichment, assembly, and activity of polyhydroxyalkanoate-synthesizing mixed microbial communities

Polyhydroxyalkanoates (PHA) are popular biopolymers due to their potential use as biodegradable thermoplastics. In this study, three aerobic sequencing batch reactors were operated identically except for their temperatures, which were set at 15 °C, 35 °C, and 48 °C. The reactors were subjected to a feast–famine feeding regime, where carbon sources are supplied intermittently, to enrich PHA-accumulating microbial consortia. The biomass was sampled for 16S rRNA gene amplicon sequencing of both DNA (during the enrichment phase) and cDNA (during the enrichment and accumulation phases). All temperatures yielded highly enriched PHA-accumulating consortia. Thermophilic communities were significantly less diverse than those at low or mesophilic temperatures. In particular, Thauera was highly adaptable, abundant, and active at all temperatures. Low temperatures resulted in reduced PHA production rates and yields. Analysis of the microbial community revealed a collapse of community diversity during low-temperature PHA accumulation, suggesting that the substrate dosing strategy was unsuccessful at low temperatures. This points to future possibilities for optimizing low-temperature PHA accumulation.

Metatranscriptomic analysis indicates prebiotic effect of isomalto/malto-polysaccharides on human colonic microbiota in-vitro

Isomalto/malto-polysaccharides (IMMPs) are a novel type of soluble dietary fibres with a prebiotic potential promoting growth of beneficial microbes in the gut. However, the mode of action of IMMPs remains unknown. Previous studies on IMMPs showed an increase in total bacteria, especially lactobacilli, and higher production of short chain fatty acids (SCFA) when IMMPs were fed to rats or used during in vitro fermentation. Here we used metatranscriptomics to investigate how IMMPs with different amounts of α − (1 → 6) glycosidic linkages affected microbial function during incubation with human fecal inoculum. We showed that active microbial community dynamics during fermentation varied depending on the type of IMMP used and that the observed changes were reflected in the community gene expression profiles. Based on metatranscriptome analysis, members of Bacteroides, Lactobacillus and Bifidobacterium were the predominant degraders of IMMPs, and the increased gene expression in these bacteria correlated with high amounts of α − (1 → 6) glycosidic linkages. We also noted an increase in relative abundance of these bacteria and an activation of pathways involved in SCFA synthesis. Our findings could provide a baseline for more targeted approaches in designing prebiotics for specific bacteria and to achieve more controlled modulation of microbial activity towards desired health outcomes.

Microbial community structure and function in a sandy soil column under dynamic hydrologic regimes

The capillary fringe (CF) exhibits steep chemical and redox gradients, representing a critical reactive interface in the subsurface. The spatial extent of the CF is temporally dynamic because of water table and soil moisture fluctuations. To simulate the spatio-temporal responses of the CF’s microbial community structure and activity, a 91 cm long sandy soil column experiment was conducted by imposing three different sequential hydrologic regimes: a stable water table separating the unsaturated and saturated zones (static regime), periodic pulse infiltration events with a constant water table position (infiltration regime), and water table fluctuations under three drainage-imbibition cycles of 6, 12, and 18 days (fluctuating regime). The investigation focused on the microbially-mediated turnover of nitrogen (N) and carbon (C). Geochemical profiles in the soil column were monitored continuously, while microbial DNA was extracted for 16S rDNA sequencing at the start, middle and end of the experiment. The observed microbial community compositions corresponded to five categories: (1) initial soil, (2) near-surface and (3) CF and saturated soil under the infiltration regime, (4) unsaturated and (5) saturated soil in the fluctuating regime. Based on co-occurrence network analysis, microbial physiologies matched the predominant geochemical conditions, and relatively stable community structures prevailed throughout the experiment. NO3- and NH4+ were more available to the microbes in the fluctuating regime’s alternating oxic/anoxic zone, leading to a more flexible network. The prevalent microbial metabolic pathways predicted using FAPROTAX were mainly associated with N and C metabolisms and significantly correlated with the taxonomic compositions. However, the dominant microbial groups were shared among all the soil samples. The limited spatial differences in microbial community structure under the fluctuating regime were likely due to a more pronounced role of microbial activity than microbial diversity, and similar drying-wetting conditions between the soil column and the filed site. Internally consistent geochemical and microbial depth stratifications were identified by (1) the redox potential and nitrogen species distributions, (2) spatial moment analysis of NO3- and NH4+ concentrations, (3) microbial community composition and (4) function. The five imposed hydrologic regimes generated distinct and coupled geochemical and microbial signatures. These signatures resulted from variations in the soil microbial community’s activity, rather than diversity or abundance.

Metabolic adaptations underpin high productivity rates in relict subsurface water

Groundwater aquifers are ecological hotspots with diverse microbes essential for biogeochemical cycles. Their ecophysiology has seldom been studied on a basin scale. In particular, our knowledge of chemosynthesis in the deep aquifers where temperatures reach 60 °C, is limited. Here, we investigated the diversity, activity, and metabolic potential of microbial communities from nine wells reaching ancient groundwater beneath Israel’s Negev Desert, spanning two significant, deep (up to 1.5 km) aquifers, the Judea Group carbonate and Kurnub Group Nubian sandstone that contain fresh to brackish, hypoxic to anoxic water. We estimated chemosynthetic productivity rates ranging from 0.55 ± 0.06 to 0.82 ± 0.07 µg C L−1 d−1 (mean ± SD), suggesting that aquifer productivity may be underestimated. We showed that 60% of MAGs harbored genes for autotrophic pathways, mainly the Calvin–Benson–Bassham cycle and the Wood–Ljungdahl pathway, indicating a substantial chemosynthetic capacity within these microbial communities. We emphasize the potential metabolic versatility in the deep subsurface, enabling efficient carbon and energy use. This study set a precedent for global aquifer exploration, like the Nubian Sandstone Aquifer System in the Arabian and Western Deserts, and reconsiders their role as carbon sinks.

Impact mechanisms of various surfactants on the biodegradation of phenanthrene in soil: Bioavailability and microbial community responses

The present study was conducted to systematically explore the mechanisms underlying the impact of various surfactants (CTAB, SDBS, Tween 80 and rhamnolipid) at different doses (10, 100 and 1000 mg/kg) on the biodegradation of a model polycyclic aromatic hydrocarbon (PAH) by indigenous soil microorganisms, focusing on bioavailability and community responses. The cationic surfactant CTAB inhibited the biodegradation of phenanthrene within the whole tested dosage range by decreasing its bioavailability and adversely affecting soil microbial communities. Appropriate doses of SDBS (1000 mg/kg), Tween 80 (100, 1000 mg/kg) and rhamnolipid at all amendment levels promoted the transformation of phenanthrene from the very slow desorption fraction (Fvslow) to bioavailable fractions (rapid and slow desorption fractions, Frapid and Fslow), assessed via Tenax extraction. However, only Tween 80 and rhamnolipid at these doses significantly improved both the rates and extents of phenanthrene biodegradation by 22.1–204.3 and 38.4–76.7 %, respectively, while 1000 mg/kg SDBS had little effect on phenanthrene removal. This was because the inhibitory effects of anionic surfactant SDBS, especially at high doses, on the abundance, diversity and activity of soil microbial communities surpassed the bioavailability enhancement in dominating biodegradation. In contrast, the nonionic surfactant Tween 80 and biosurfactant rhamnolipid enhanced the bioavailability of phenanthrene for degradation and also that to specific degrading bacterial genera, which stimulated their growth and increased the abundance of the related nidA degradation gene. Moreover, they promoted the total microbial/bacterial biomass, community diversity and polyphenol oxidase activity by providing available substrates and nutrients. These findings contribute to the design of suitable surfactant types and dosages for mitigating the environmental risk of PAHs and simultaneously benefiting microbial ecology in soil through bioremediation.

Nitrogen removal pathways in lake restoration using microalgal-bacterial granular sludge: Unraveling influence of organics and carbon to nitrogen ratio

This study investigated the performance of microalgal-bacterial granular sludge (MBGS) in the restoration of Qingling Lake and Huangjia Lake, focusing on nitrogen removal under varying water quality conditions. Significant color changes in MBGS and differences in granule characteristics were observed, with Qingling Lake demonstrating superior removal efficiencies for ammonia nitrogen, nitrate nitrogen, and total nitrogen compared to Huangjia Lake. Stoichiometric analysis revealed that when the chemical oxygen demand (COD) and carbon-to-nitrogen (C/N) ratios were less than 20 mg/L and 20, respectively, assimilatory nitrate reduction was positively correlated with both, whereas denitrification was negatively correlated. Gene function analysis showed that Qingling Lake had a more active microbial community supporting efficient nitrogen metabolism. The findings highlighted the enormous potential of MBGS in lake restoration, demonstrating its ability to adapt to different COD concentrations and C/N ratios by altering its nitrogen removal pathways.