Microbial Community Activity Research Articles

Comparative study of exoelectrogenic utilization preferences and hydrogen conversion among major fermentation products in microbial electrolysis cells

This study comparatively investigated the exoelectrogenic utilization and hydrogen conversion of major dark fermentation products (acetate, propionate, butyrate, lactate, and ethanol) from organic wastes in dual-chamber microbial electrolysis cells (MECs) alongside their mixture as a simulated dark fermentation effluent (DFE). Acetate-fed MECs showed the highest hydrogen yield (1,465 mL/g chemical oxygen demand), near the theoretical maximum yield, with the highest coulombic efficiency (105%) and maximum current density (7.9 A/m2), followed by lactate-fed, propionate-fed, butyrate-fed, mixture-fed, and ethanol-fed MECs. Meanwhile, the highest hydrogen production rate (514 mL/L anolyte∙d) was observed in ethanol-fed MECs despite their lower coulombic efficiency. Butyrate was the least favored substrate, followed by propionate, leading to significantly delayed startup and reaction. The active anodic microbial community structure varied considerably among the MECs utilizing different substrates, particularly between Geobacter and Acetobacterium dominance. The results highlight the substantial effect of the DFE composition on its utilization and current-producing bioanode development.

Active soil microbial composition and proliferation are directly affected by the presence of biocides from building materials

Combinations of biocides are commonly added to building materials to prevent microbial growth and thereby cause degradation of the façades. These biocides reach the environment by leaching from façades posing an environmental risk. Although ecotoxicity to the aquatic habitat is well established, there is hardly any data on the ecotoxicological effects of biocides on the soil habitat. This study aimed to characterize the effect of the biocides terbutryn, isoproturon, octhilinone, and combinations thereof on the total and metabolically active soil microbial community composition and functions. Total soil microbial community was retrieved directly from the nucleic acid extracts, while the DNA of the active soil microbial community was separated after bromodeoxyuridine labeling. Bacterial 16S rRNA gene and fungal internal transcribed spacer region gene-based amplicon sequencing was carried out for both active and total, while gene copy numbers were quantified only for the total soil microbial community. Additionally, soil respiration and physico-chemical parameters were analyzed to investigate overall soil microbial activity. The bacterial and fungal gene copy numbers were significantly affected by single biocides and combined biocide soil treatment but not soil respiration and physico-chemical parameters. While the total soil microbiome experienced only minor effects from single and combined biocide treatment, the active soil microbiome was significantly impacted in its diversity, richness, composition, and functional patterns. The active bacterial richness was more sensitive than fungal richness. However, the adverse effects of the biocide combination treatments on soil bacterial richness were highly dependent on the identities of the biocide combination. Our results demonstrate that the presence of biocides frequently used in building materials affects the active soil microbiome. Thereby, the approach described herein can be used as an ecotoxicological measure for the effect on complex soil environments in future studies.

Cover crop-mediated soil carbon storage and soil health in semi-arid irrigated cropping systems

Cover cropping is considered a climate-smart strategy to regenerate low-fertility soils in arid and semi-arid regions. However, the mechanisms of soil organic carbon (SOC) storage and soil health improvement in semi-arid irrigated cropping systems are poorly understood. The main goal of this study was to evaluate cover crop effects on various physical, chemical, and biological indicators of soil health in an irrigated silage corn (Zea mays L.)–sorghum [Sorghum bicolor (L.) Moench] rotation and understanding how changes in soil health contribute to SOC storage. We evaluated various SOC and nitrogen (N) pools, and microbial community structure under cover crop mixture of grasses, brassicas, and legumes (GBL), grasses and brassicas (GB), grasses and legumes (GL), and no cover crops (NCC) control for four years. Grasses included annual ryegrass (Lolium multiflorum Lam.) and winter triticale (× Triticosecale Wittmack), brassicas included turnip (Brassica rapa subsp. rapa L.) and daikon radish (Raphanus sativus var. Longipinnatus Bailey), and legumes included pea (Pisum sativum subsp. arvense L.) and berseem clover (Trifolium alexandrinum L.). Soil C pools: SOC, potentially mineralizable C, microbial biomass C, mineral-associated organic C (MAOC), and particulate organic C (POC) were greater with cover crops than without, but the effects were not consistent in all study years. Soil organic N was also greater under cover crops than under NCC. Soil C-to-N (C:N) ratio increased over the years but was similar among treatments. Cover crops used N and soil water to grow, significantly reducing soil inorganic N content and water-filled pore spaces in the first two years. However, fungal and bacterial communities grew better under cover crops with a high fungi-to-bacteria ratio than under NCC. The soil MAOC content was related to microbial community and enzyme activity while POC was affected by soil physicochemical conditions, specifically soil pH and mineral N availability, highlighting two major pathways of SOC sequestration in semi-arid cropping systems. This study showed how cover crops enhance SOC storage and soil health in semi-arid cropping systems.

Metatranscriptomic characterization of six types of forensic samples and its potential application to body fluid/tissue identification: A pilot study

Microorganisms are potential markers for identifying body fluids (venous and menstrual blood, semen, saliva, and vaginal secretion) and skin tissue in forensic genetics. Existing published studies have mainly focused on investigating microbial DNA by 16 S rRNA gene sequencing or metagenome shotgun sequencing. We rarely find microbial RNA level investigations on common forensic body fluid/tissue. Therefore, the use of metatranscriptomics to characterize common forensic body fluids/tissue has not been explored in detail, and the potential application of metatranscriptomics in forensic science remains unknown. Here, we performed 30 metatranscriptome analyses on six types of common forensic sample from healthy volunteers by massively parallel sequencing. After quality control and host RNA filtering, a total of 345,300 unigenes were assembled from clean reads. Four kingdoms, 137 phyla, 267 classes, 488 orders, 985 families, 2052 genera, and 4690 species were annotated across all samples. Alpha- and beta-diversity and differential analysis were also performed. As a result, the saliva and skin groups demonstrated high alpha diversity (Simpson index), while the venous blood group exhibited the lowest diversity despite a high Chao1 index. Specifically, we discussed potential microorganism contamination and the “core microbiome,” which may be of special interest to forensic researchers. In addition, we implemented and evaluated artificial neural network (ANN), random forest (RF), and support vector machine (SVM) models for forensic body fluid/tissue identification (BFID) using genus- and species-level metatranscriptome profiles. The ANN and RF prediction models discriminated six forensic body fluids/tissue, demonstrating that the microbial RNA-based method could be applied to BFID. Unlike metagenomic research, metatranscriptomic analysis can provide information about active microbial communities; thus, it may have greater potential to become a powerful tool in forensic science for microbial-based individual identification. This study represents the first attempt to explore the application potential of metatranscriptome profiles in forensic science. Our findings help deepen our understanding of the microorganism community structure at the RNA level and are beneficial for other forensic applications of metatranscriptomics.

Long-term impact of nano zero-valent iron on methanogenic activity, microbial community structure, and transcription activity in anaerobic wastewater treatment system

Nano zero-valent iron (NZVI) is commonly used in industrial wastewater treatment. However, its long-term impact mechanisms of metabolization in anaerobic systems are not well understood. This study investigated the effects of long-term and continuous addition of NZVI on methanogenic activity, microbial community, and transcription activity. The results demonstrated that low levels of NZVI (1000 mg/L) induced inhibition of methanogenesis after 80 days, while high levels of NZVI (5000 mg/L) immediately led to a sharp decrease of cumulative methane production and chemical oxygen demand removal, which arrived at a steady state (14.4 % of control and 17 %) after 30 days. NZVI adversely affected cell viability, adenosine triphosphate production, and fatty acid evolution of cell membranes played a crucial role in resisting chronic NZVI toxicity. Moreover, high NZVI levels hindered the transcription of key enzymes CoM and mcrA, while low NZVI levels maintained its high CoM and mcrA activity, but down-regulated the transcription of cdh and hdr. Besides, amino-utilizing bacteria was reduced under the high NZVI concentration, while low NZVI changed dominant genus with potential protein hydrolysis function from Candidatus Cloacamonas to Sedimentibacter. These results provide a guideline for proper NZVI utilization in wastewater treatment.

Enrichment of Aerobic and Anaerobic Hydrocarbon-Degrading Bacteria from Multicontaminated Marine Sediment in Mar Piccolo Site (Taranto, Italy).

Marine sediments act as a sink for the accumulation of various organic contaminants such as polychlorobiphenyls (PCBs). These contaminants affect the composition and activity of microbial communities, particularly favoring those capable of thriving from their biodegradation and biotransformation under favorable conditions. Hence, contaminated environments represent a valuable biological resource for the exploration and cultivation of microorganisms with bioremediation potential. In this study, we successfully cultivated microbial consortia with the capacity for PCB removal under both aerobic and anaerobic conditions. The source of these consortia was a multicontaminated marine sediment collected from the Mar Piccolo (Taranto, Italy), one of Europe's most heavily polluted sites. High-throughput sequencing was employed to investigate the dynamics of the bacterial community of the marine sediment sample, revealing distinct and divergent selection patterns depending on the imposed reductive or oxidative conditions. The aerobic incubation resulted in the rapid selection of bacteria specialized in oxidative pathways for hydrocarbon transformation, leading to the isolation of Marinobacter salinus and Rhodococcus cerastii species, also known for their involvement in aerobic polycyclic aromatic hydrocarbons (PAHs) transformation. On the other hand, anaerobic incubation facilitated the selection of dechlorinating species, including Dehalococcoides mccartyi, involved in PCB reduction. This study significantly contributes to our understanding of the diversity, dynamics, and adaptation of the bacterial community in the hydrocarbon-contaminated marine sediment from one sampling point of the Mar Piccolo basin, particularly in response to stressful conditions. Furthermore, the establishment of consortia with biodegradation and biotransformation capabilities represents a substantial advancement in addressing the challenge of restoring polluted sites, including marine sediments, thus contributing to expanding the toolkit for effective bioremediation strategies.

Temporal Variability in Soil Greenhouse Gas Fluxes and Influencing Factors of a Primary Forest on the Eastern Qinghai-Tibetan Plateau

Soil greenhouse gas (GHG) fluxes relate to soil carbon and nitrogen budgets and have a significant impact on climate change. Nevertheless, the temporal variation and magnitude of the fluxes of all three major GHGs (CO2, CH4 and N2O) and their influencing factors have not been elucidated clearly in primary forests on the eastern Qinghai-Tibetan Plateau. Herein, field chamber GHG fluxes from May to November, soil microbial community and enzyme activity were analyzed in a fir-dominated (Abies fargesii var. faxoniana) primary forest. The emission rates of CO2 and N2O ranged between 64.69–243.22 mg CO2 m−2 h−1 and 1.69–5.46 ug N2O m−2 h−1, exhibiting a temporally unimodal pattern with a peak in July. The soil acted as a CH4 sink, and the uptake rate varied between 52.96 and 84.67 μg CH4 m−2 h−1 with the higher uptake rates in June and November. The temporal variation in the CO2 flux was significantly correlated with the geometric mean of enzyme activities, suggesting that the soil CO2 flux was determined by microbial activity rather than soil microbial biomass. The soil N2O flux was positively related to nitrate concentration with marginal significance, probably because N2O was a byproduct of nitrification and denitrification processes. The soil CH4 uptake was closely associated with methanotrophic biomass (18:1ω7c). The results highlight divergent temporal dynamics of GHG fluxes owing to different driving mechanisms and an important CH4 sink in the primary forest soil, helping to evaluate the carbon and nitrogen budgets of primary forests on the eastern Qinghai-Tibetan Plateau.

Ecological function and interaction of different bacterial groups during alginate processing in coastal seawater community

The degradation of high molecular weight organic matter (HMWOM) is a core process of oceanic carbon cycle, which is determined by the activity of microbial communities harboring hundreds of different species. Illustrating the active microbes and their interactions during HMWOM processing can provide key information for revealing the relationship between community composition and its ecological functions. In this study, the genomic and transcriptional responses of microbial communities to the availability of alginate, an abundant HMWOM in coastal ecosystem, were elucidated. The main degraders transcribing alginate lyase (Aly) genes came from genera Alteromonas, Psychrosphaera and Colwellia. Meanwhile, some strains, mainly from the Rhodobacteraceae family, did not transcribe Aly gene but could utilize monosaccharides to grow. The co-culture experiment showed that the activity of Aly-producing strain could promote the growth of Aly-non-producing strain when alginate was the sole carbon source. Interestingly, this interaction did not reduce the alginate degradation rate, possibly due to the easily degradable nature of alginate. This study can improve our understanding of the relationship between microbial community activity and alginate metabolism function as well as further manipulation of microbial community structure for alginate processing.

Different responses of mesophilic and thermophilic anaerobic digestion of waste activated sludge to PVC microplastics.

The effect of microplastics (MPs) retained in waste activated sludge (WAS) on anaerobic digestion (AD) performance has attracted more and more attention. However, their effect on thermophilic AD remains unclear. Here, the influence of polyvinyl chloride (PVC) MPs on methanogenesis and active microbial communities in mesophilic (37 °C) and thermophilic (55 °C) AD was investigated. The results showed that 1, 5, and 10 mg/L PVC MPs significantly promoted the cumulative methane yield in mesophilic AD by 5.62%, 7.36%, and 8.87%, respectively, while PVC MPs reduced that in thermophilic AD by 13.30%, 18.82%, and 19.99%, respectively. Moreover, propionate accumulation was only detected at the end of thermophilic AD with PVC MPs. Microbial community analysis indicated that PVC MPs in mesophilic AD enriched hydrolytic and acidifying bacteria (Candidatus Competibacter, Lentimicrobium, Romboutsia, etc.) together with acetoclastic methanogens (Methanosarcina, Methanosaeta). By contrast, most carbohydrate-hydrolyzing bacteria, propionate-oxidizing bacterium (Pelotomaculum), and Methanosarcina were inhibited by PVC MPs in thermophilic AD. Network analysis further suggested that PVC MPs significantly changed the relationship of key microorganisms in the AD process. A stronger correlation among the above genera occurred in mesophilic AD, which may promote the methanogenic performance. These results suggested that PVC MPs affected mesophilic and thermophilic AD of WAS via changing microbial activities and interaction.

Microbial community and enzyme activity respond differently to seasonal and edaphic factors in forest and grassland ecosystems

Although microbial community and function patterns have been extensively studied, little is known about whether the patterns are consistent in different ecosystems and how they are influenced by seasonality or other environmental factors. To test the driving factors of microbial communities and potential functions, we collected soil samples from five forests (mixed broadleaved-Korean pine forest, mixed pine and oak forest, deciduous broadleaved mixed forest, subtropical evergreen broad-leaved forest and tropical rainforest) and three grassland ecosystems (meadow steppe, semi-arid grassland and arid grassland) across China in three seasons (spring, summer and autumn). Microbial diversity based on the sequencing of 16S rRNA gene for bacteria and internal transcribed spacer (ITS) genes for fungi were measured, and potential functions represented by soil extracellular enzyme activities (EEAs) were analyzed. The results found that soil EEAs were significantly higher in summer than in spring and autumn, and both bacterial and fungal richness indices showed greater seasonal fluctuations than the diversity. Fungal richness indices were highest in summer in both forest and grassland ecosystems, while the lowest were observed in spring for forest and in autumn for grassland, respectively. In addition, fungal communities were closely related to ecosystem types, while bacterial communities were not significantly different across ecosystems and exhibited a broader habitat niche breadth, but the relative abundance of dominant bacterial phyla showed stronger correlations with environmental variables (including climate, soil properties and nutrients) in grassland than in forest ecosystems. The decoupling of microbial community and EEAs was observed in both forest and grassland ecosystems, indicating the function redundancy of soil microorganisms. The present study provided crucial information about the effects of ecosystem types, seasonality and edaphic factors on soil microbial communities and EEAs, and could advance the understanding of soil potential function responses to environmental changes.

Microaerobic methane-driven denitrification in a biotrickle bed – Investigating the active microbial biofilm community composition using RNA-stable isotope probing

A microaerobic (2% O2 v/v) biotrickle bed reactor supplied continuously with 2% methane to drive nitrate removal (MAME-D) was investigated using 16S rDNA and rRNA amplicon sequencing in combination with RNA-stable isotope probing (RNA-SIP) to identify the active microorganisms. Methane removal rates varied from 500 to 1000 mmol m−3h−1 and nitrate removal rates from 25 to 58 mmol m−3h−1 over 55 days of operation. Biofilm samples from the column were incubated in serum bottles supplemented with 13CH4. 16S rDNA analysis indicated a simple community structure in which four taxa accounted for 45% of the total relative abundance (RA). Dominant genera included the methanotroph Methylosinus and known denitrifiers Nubsella and Pseudoxanthomonas; along with a probable denitrifier assigned to the order Obscuribacterales. The 16S rRNA results revealed the methanotrophs Methylocystis (15% RA) and Methylosinus (10% RA) and the denitrifiers Arenimonas (10% RA) and Pseudoxanthomonas (7% RA) were the most active genera. Obscuribacterales was the most active taxa in the community at 22% RA. Activity was confirmed by the Δ buoyant density changes with time for the taxa, indicating most of the community activity was associated with methane oxidation and subsequent consumption of methanotrophic metabolic intermediates by the denitrifiers. This is the first report of RNA stable isotope probing within a microaerobic methane driven denitrification system and the active community was markedly different from the full community identified via 16S-rDNA analysis.

Effect of carbon nanomaterials on functional diversity and structure of soil microbial community under single and repeated exposures.

The extensive application of carbon nanomaterials (CNMs) has attracted increasing studies concerned about its environmental impact. These studies focus on single exposure to CNMs, but repeated exposures with relatively low concentration are more likely to occur under actual exposure scenario. In this study, we studied the metabolic functional and structure of soil microorganism community under single and repeated exposures to multiwalled carbon nanotubes (MW), graphene (GR), and fullerene (C60) by Biolog EcoPlates and high-throughput sequencing. Our findings revealed that repeated exposures to CNMs significantly increase the metabolic activity and diversity of the soil microbial community as compared with single exposure. Principal component and similarity analysis not only indicated that GR exerted a stronger effect on soil microbial diversity among three exposures compared to C60 and MW, but also revealed that the metabolic activity of the soil microbial community was more affected by the exposure scenarios of CNMs than the type of CNMs. These findings elucidated the effect of CNMs under different exposure scenarios on soil microorganism community, providing a new perspective on the risk assessment of nanomaterials.

Biochemical, Catabolic, and PGP Activity of Microbial Communities and Bacterial Strains from the Root Zone of Baccharis linearis in a Mediterranean Mine Tailing.

The management of mine tailings (MT) is commonly workload heavy, intrusive, and expensive. Phytostabilization offers a promising approach for MT management; however, it poses challenges due to the unfavorable physicochemical properties of these wastes. Nevertheless, native microorganisms capable of supporting plant growth and development could enhance the efficacy of phytostabilization. This study assesses the biological activity of microbial communities from the root zone of Baccharis linearis, which is naturally present in MT, in order to evaluate their biotechnological potential for phytostabilization. The root zone and bulk samples were collected from B. linearis plants located within a MT in the Mediterranean zone of Chile. Enzyme activities related to the cycling of C, N, and P were assessed. The community-level physiological profile was evaluated using the MicroRespTM system. Bacterial plant growth-promoting (PGP) traits and colony forming units (CFU) were evaluated through qualitative and microbiological methods, respectively. CFU, enzyme activities, and CLPP were higher in the root zone compared with the bulk samples. Five bacterial strains from the root zone exhibited PGP traits such as P solubilization and N acquisition, among others. The presence of microbial communities in the root zone of B. linearis with PGP traits suggests their potential to enhance the ecological management of MT through phytostabilization programs.

Longitudinal Microbiome Changes in Supragingival Biofilm Transcriptomes Induced by Orthodontics.

Common oral diseases are known to be associated with dysbiotic shifts in the supragingival microbiome, yet most oral microbiome associations with clinical end points emanate from cross-sectional studies. Orthodontic treatment is an elective procedure that can be exploited to prospectively examine clinically relevant longitudinal changes in the composition and function of the supragingival microbiome. A longitudinal cohort study was conducted among 24 adolescent orthodontic patients who underwent saliva and plaque sampling and clinical examinations at time points: before fixed appliance bonding and at 1, 6, and 12 wk thereafter. Clinical indices included bleeding on probing (BOP), mean gingival index (GI), probing depths (PDs), and plaque index (PI). To study the biologically (i.e., transcriptionally) active microbial communities, RNA was extracted from plaque and saliva for RNA sequencing and microbiome bioinformatics analysis. Longitudinal changes in microbiome beta diversity were examined using PERMANOVA tests, and the relative abundance of microbial taxa was measured using Kruskal-Wallis tests, Wilcoxon rank-sum tests, and negative binomial and zero-inflated mixed models. Clinical measures of oral health deteriorated over time-the proportion of sites with GI and PI ≥1 increased by over 70% between prebonding and 12 wk postbonding while the proportion of sites with PD ≥4 mm increased 2.5-fold. Streptococcus sanguinis, a health-associated species that antagonizes cariogenic pathogens, showed a lasting decrease in relative abundance during orthodontic treatment. Contrarily, caries- and periodontal disease-associated taxa, including Selenomonas sputigena, Leptotrichia wadei, and Lachnoanaerobaculum saburreum, increased in abundance after bonding. Relative abundances of Stomatobaculum longum and Mogibacterium diversum in prebonding saliva predicted elevated BOP 12 wk postbonding, whereas Neisseria subflava was associated with lower BOP. This study offers insights into longitudinal community and species-specific changes in the supragingival microbiome transcriptome during fixed orthodontic treatment, advancing our understanding of microbial dysbioses and identifying targets of future health-promoting clinical investigations. Bonding braces was associated with subsequent changes in the oral microbiome characterized by increases in disease-associated species, decreases in health-associated species, and worsened clinical measures of oral health.

Composition and activity of soil microbial communities in native and non-native vegetation of southern California

The proliferation of non-native plant species in novel habitats has altered plant community diversity, ecosystem carbon (C) and nutrient cycling, and disturbance regimes worldwide. However, the impacts of non-native plants on soil microbial community composition and activity are still poorly known, especially in semi-arid woodlands. Here we utilized next generation sequencing (16S rRNA sequencing of the V3-V4 regions) and measurements of microbial activity (respiration, net N mineralization, and enzyme assays) to determine how soil microbial composition and activity varied between native and non-native vegetation patches in coastal sage scrub (CSS) woodlands. We sampled eight CSS sites and collected topsoil (0–10 cm) samples from six paired native and non-native vegetation patches at each site. Native patches had significantly (p < 0.05) higher vegetation cover, dissolved organic C (DOC), and dissolved inorganic nitrogen (DIN) concentrations than non-native patches. β-glucosidase activity was significantly higher (ca. 10 nM g−2 h−1) and peroxidase activity was significantly lower (ca. 60 nM g−2 h−1) in non-native vegetation, while rates of net N mineralization and nitrification, phosphatase and NAGase activities, and respiration were not significantly different in native and non-native vegetation but were positively correlated with total soil C and N (r > 0.60; p < 0.05). Bacterial alpha- and beta-diversity were not significantly different (p > 0.05) between native and non-native patches; however, bacteria/archaea in the phyla Gemmatimonadota, Planctomycetota, Armatimonadota, Fibrobacterota, Thermoplasmatota, and Entotheonellaeota were over-expressed in non-native patches. Within these phyla there were 20 orders that were differentially expressed in native or non-native vegetation, and more than half (60 %) had significantly higher relative abundance in native vegetation. Our results indicate that the expansion of non-native vegetation in semi-arid woodlands significantly alters soil C and N, which feeds back on microbial activity and community composition.

Glacial secrets uncovered: Revealing the modes of survival of metabolically active microbial communities entrapped in polar glacial ice

Glacial secrets uncovered: Revealing the modes of survival of metabolically active microbial communities entrapped in polar glacial ice

Differences among active toluene-degrading microbial communities in farmland soils with different levels of heavy metal pollution.

Heavy metals can severely influence the mineralisation of organic pollutants in a compound-polluted environment. However, to date, no study has focused on the effects of heavy metals on the active organic pollutant-degrading microbial communities to understand the bioremediation mechanism. In this study, toluene was used as the model organic pollutant to explore the effects of soils with different levels of heavy metal pollution on organic contaminant degradation in the same area via stable isotope probing (SIP) and 16S rRNA high-throughput sequencing. Heavy metals can seriously affect toluene biodegradation and regulate the abundance and diversity of microbial communities. SIP revealed a drastic difference in the community structure of active toluene degraders between the unpolluted and heavy metal-polluted soils. All SIP-identified degraders were assigned to nine bacterial classes, among which Alphaproteobacteria, Gammaproteobacteria, and Bacilli were shared by both treatments. Among all active degraders, Nitrospira, Nocardioides, Conexibacteraceae, and Singulisphaera were linked to toluene biodegradation for the first time. Notably, the type of active degrader and microbial diversity were strongly related to biodegradation efficiency, indicating their key role in toluene biodegradation. Overall, heavy metals can affect the microbial diversity and alter the functional microbial communities in soil, thereby influencing the removal efficiency of organic contaminants. Our findings provide novel insights into the biodegradation mechanism of organic pollutants in heavy metal-polluted soils and highlight the biodiversity of microbes involved in toluene biodegradation in compound-polluted environments.

Drifting in the deep: Metatranscriptomics and metabarcoding reveal sustained metabolic activity and community composition in hydrothermal vent plume microbial communities

The deep sea is the largest habitat on our planet, supporting a vast diversity of organisms which have yet to be fully described. This habitat is punctuated by hydrothermal vents in which energy derived from chemosynthesis drives carbon fixation, supporting a complex and rich food web. Connectivity between vent systems remains an active area of research, with questions as to how vent-influenced microbial function and diversity persists over space and time. In particular, the role hydrothermal vent plumes play as potential highways for connectivity and biogeography is not well understood. To add to the growing body of research, this study sampled plume waters above the Moytirra hydrothermal vent field, located just north of the Azores. We examined how hydrothermal vent plume community biodiversity and metabolic activities change with distance from the vent using a combination of metabarcoding and metatranscriptomic sequencing. We detected a rich diversity of both prokaryotic and eukaryotic organisms inhabiting the plume, which remained metabolically active for kilometers from the vent source. Enriched sulfur metabolism functional signals and relative abundance of sulfur oxidizing bacteria suggest reduced sulfur compounds are a fundamental energy source within plume waters. Additionally, we observed evidence of top-down controls on primary production through both known grazers and putative viral activity. Although community-level functional signals suggest active metabolic functions for over a kilometer north or south of the vent field, these functions grew increasingly dissimilar to those observed directly above the vent site, and bacterial communities displayed indications of entering quiescent stages, likely due to decreasing resources and reduced temperatures. These data provide a first glimpse of Moytirra’s microbial biodiversity, in addition to providing a high-resolution understanding of life on the drift within a hydrothermal plume, its persistence with distance, and implications for connectivity.

Metabolically Active Microbial Communities in Oilfields: A Systematic Review and Synthesis of RNA Preservation, Extraction, and Sequencing Methods

Characterizing metabolically active microorganisms using RNA-based methods is a crucial tool for monitoring and mitigating operational issues, such as oil biodegradation and biocorrosion of pipelines in the oil and gas industry. Our review, a pioneering study, addresses the main methods used to preserve, isolate, and sequence RNA from oilfield samples and describes the most abundant metabolically active genera studied. Using the MEDLINE/PubMed, PubMed Central, Scopus, and Web of Science databases, 2.561 potentially eligible records were identified. After screening, 20 studies were included in our review, underscoring the scarcity of studies related to the subject. Data were extracted and reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA). These studies evaluated different samples, including produced water (PW), injection water (IW), solid deposits (SD), oil (OIL), and oily sludge (OS) collected from oilfields located in Australia, China, India, Mexico, and the United Arab Emirates. Environmental samples accounted for 55% of the studies, while enriched cultures and microbial consortia represented 35% and 15% of studies, respectively. PW was the most frequently studied sample, comprising 72% of all samples. Filtration and centrifugation were the only processes employed to concentrate the biomass present in samples. For RNA preservation, the most used method was a solution composed of 95:5 v/v ethanol/TRIzol, while for RNA isolation, the TRIzol reagent was the most cited. The Sanger sequencing method was used in all studies evaluating functional genes (alkB, dsrA, aprA, assA, and mcrA), and the Next-Generation Sequencing (NGS) method was employed in studies for sequencing transcripts of the 16S rRNA gene and metatranscriptomes. Pseudomonas (16S rRNA = PW: 2%; IW: 8%; metatranscriptome = PW: 20%) and Acinetobacter (16S rRNA = PW: 1%; IW: 4%; metatranscriptome = PW: 17%) were the most abundant genera. This study outlined the primary methods employed in researching metabolically active microorganisms. These data provide a foundation for future research. However, it is essential to note that we cannot yet determine the most effective method. We hope that this study will inspire further research related to the standardization of RNA preservation, extraction, and sequencing methods and significantly contribute to our understanding of active microbial communities in oilfields.

Abrupt permafrost thaw triggers activity of copiotrophs and microbiome predators.

Permafrost soils store a substantial part of the global soil carbon and nitrogen. However, global warming causes abrupt erosion and gradual thaw, which make these stocks vulnerable to microbial decomposition into greenhouse gases. Here, we investigated the microbial response to abrupt in situ permafrost thaw. We sequenced the total RNA of a 1m deep soil core consisting of up to 26'500-year-old permafrost material from an active abrupt erosion site. We analysed the microbial community in the active layer soil, the recently thawed, and the intact permafrost, and found maximum RNA: DNA ratios in recently thawed permafrost indicating a high microbial activity. In thawed permafrost, potentially copiotrophic Burkholderiales and Sphingobacteriales, but also microbiome predators dominated the community. Overall, both thaw-dependent and long-term soil properties significantly correlated with changes in community composition, as did microbiome predator abundance. Bacterial predators were dominated in shallower depths by Myxococcota, while protozoa, especially Cercozoa and Ciliophora, almost tripled in relative abundance in thawed layers. Our findings highlight the ecological importance of a diverse inter-kingdom and active microbial community highly abundant in abruptly thawing permafrost, as well as predation as potential biological control mechanism.