Indigenous Microbial Communities Research Articles

Soil biodiversity and microbial antagonism for suppression of plant-parasitic nematodes

Abstract Plant parasitic nematodes (PPN) cause significant economic losses in agriculture and the use of nematicides is the most common management practice applied today. However, due to the impact of such chemicals, more sustainable methods are needed. Current trends consider the exploitation of indigenous soil microbial communities. In this review we discuss some concepts required for the conservation and management of soil microorganisms, considered as a fundamental natural resource. Co-evolution and co-speciation are basic evolutionary processes of soil taxa involved in soil ecosystem services such as nematode regulation. The microorganisms showing a host-parasite co-evolution hold potential for the insurgence or re-construction of a natural equilibrium in soil, aiming at nematode regulation. The impact on soil microbial diversity of farming intensification and PPN management through nematicides is also discussed. Some examples of soil microbial resources and their impact including antagonists like nematophagous fungi (NF), aquatic parasites and bacteria are also briefly reviewed.

Microbial solutions must be deployed against climate catastrophe.

Injecting H2 in deep underground to store this energy carrier will produce artificial subsurface lithoautotrophic microbial ecosystems that modify the taxonomic diversity of indigenous microbial communities and their metabolic activities.

Control of dissolved H2 concentration enhances electron generation, transport and TCE reduction by indigenous microbial community

Electrokinetic enhanced bioremediation (EK-Bio) is practical for trichloroethene (TCE) dechlorination because the cathode can produce a wide range of dissolved H2 (DH) concentrations of 1.3–0 mg/L from the electrode to the aquifer. In this study, TCE dechlorination was investigated under different DH concentrations. The mechanisms were discussed by analyzing the microbial community structure and abundance of organohalide-respiring bacteria (OHRB) using 16S rRNA, and the gene abundances of key enzymes in the TCE electron transport chain using metagenomic analysis. The results showed that the moderate DH concentration of 0.19–0.53 mg/L exhibited the most pronounced TCE dechlorination, even better than the higher DH concentrations, due to the optimal redox environment, the enrichments of OHRB, reductive dehalogenase (rdhA) genes and key enzyme genes in the electron generation and transport chain. More electrons were obtained from H2 metabolism by Dehalobacter by promoting the formation of [NiFe] hydrogenase (HupS/L/C) or from glycolysis by versatile OHRB by stimulating the formation of formate and enriching formate dehydrogenase (FDH) under moderate DH conditions. In addition, the enhanced amino acid metabolism improved the vitamin K cycle for electron transport and enriched the reductive dechlorinating enzyme (RDase) genes. This study identifies the optimal DH concentration that facilitates bioremediation efficiency, provides insights into microbial community shifts and key enzymatic pathways in EK-Bio remediation.

Behind the scenes: metagenomic analysis of bacterial communities in sustainable depilation of sheepskin.

The leather industry is embracing eco-friendly technologies for both regulatory compliance and sustainable growth. While enzymatic depilation provides a greener alternative to traditional beamhouse methods, its complexity often leads to higher costs. To address this, we examined the performance of sheepskins' native bacterial flora in acetic acid conditions with low-environmental impact. Utilizing metagenomic techniques, we analyzed the bacterial community dynamics during the depilation process. This investigation revealed a notable increase in microbial diversity and richness in acetic acid treatments compared to water treatments. At the class level, a post-processing decrease in Gammaproteobacteria dominance was observed, while Actinomycetia numbers surged in the acetic acid group. In contrast, the water group showed an increase in Bacteroidia. Order-level analysis indicated reductions in Pseudomonadales and increases in Actinomycetales with acetic acid treatment, whereas Flavobacteriales was more prevalent in water-treated liquors. At the family level, Moraxellaceae decreased and Micrococcaceae increased in the acetic acid group, in contrast to the marked rise of Weeksellaceae in the water group. Temporal analyses further highlighted the evolving bacterial landscapes under different treatments. Moreover, acetic acid treatment fostered a stable microbial community, beneficial for sustainable leather processing. Functional pathways were predicted using PICRUSt2. It showed that significantly enriched degradation pathways in the water group were less abundant in the acetic acid group, potentially preventing substrate matrix damage during depilation. The study underscores the transformative potential of acetic acid for the leather industry, offering a pathway to reduce pollution while maintaining economic viability. By enhancing our understanding of microbial interactions during depilation, this study opens avenues for refining these eco-friendly techniques. Our findings advocate for a shift towards greener depilation methods and contribute to the broader dialogue on sustainable manufacturing practices, emphasizing the importance of leveraging indigenous microbial communities for environmental and economic gains.

Assembly and functional profile of rhizosphere microbial community during the Salix viminalis-AMF remediation of polycyclic aromatic hydrocarbon polluted soils

Arbuscular mycorrhizal fungi (AMF) are positive to the phytoremediation by improving plant biomass and soil properties. However, the role of AM plants to the remediation of polycyclic aromatic hydrocarbons (PAHs) is yet to be widely recognized, and the impact of AM plants to indigenous microbial communities during remediation remains unclear. In this work, a 90-day study was conducted to assess the effect of AMF-Salix viminalis on the removal of PAHs, and explore the impact to the microbial community composition, abundance, and function. Results showed that AMF-Salix viminalis effectively enhanced the removal of benzo[a]pyrene, and enriched more PAH-degrading bacteria, consisting of Actinobacteria, Chloroflexi, Sphingomonas, and Stenotrophobacter, as well as fungi including Basidiomycota, Pseudogymnoascus, and Tomentella. For gene function, AM willow enhanced the enrichment of genes involved in amino acid synthesis, aminoacyl-tRNA biosynthesis, and cysteine and methionine metabolism pathways. F. mosseae inoculation had a greater effect on alpha- and beta-diversity of microbial genes at 90 d. Additionally, AMF inoculation significantly increased the soil microbial biomass carbon and organic matter concentration. All together, the microbial community assembly and function shaped by AM willow promoted the dissipation of PAHs. Our results support the effectiveness of AM remediation and contribute to reveal the enhancing-remediation mechanism to PAHs using multi-omics data.

Plant growth-promoting rhizobacteria enhance active ingredient accumulation in medicinal plants at elevated CO2 and are associated with indigenous microbiome.

Plant growth-promoting rhizobacteria (PGPR) and elevated CO2 (eCO2) have demonstrated their individual potential to enhance plant yield and quality through close interaction with rhizosphere microorganisms and plant growth. However, the efficacy of PGPR under eCO2 on rhizosphere microbiome and, ultimately, plant yield and active ingredient accumulation are not yet fully understood. This study investigated how the medicinal plant Pseudostellaria heterophylla (P. heterophylla) and its rhizosphere microbes respond to PGPR (Bacillus subtilis and Pseudomonas fluorescens) at eCO2 (1,000 ppm). It was found that the yield and active ingredient polysaccharides accumulation in the tuber of P. heterophylla were significantly increased by 38 and 253%, respectively. This promotion has been associated with increased root development and changes in the indigenous microbial community. Metagenomics analysis revealed a significant reduction in pathogenic Fusarium abundance in the rhizosphere. Potential biocontrol bacteria Actinobacteria and Proteobacteria were enriched, especially the genera Bradyrhizobium and Rhodanobacter. The reshaping of the rhizosphere microbiome was accompanied by the upregulation of biological pathways related to metabolite biosynthesis in the rhizosphere. These modifications were related to the promotion of the growth and productivity of P. heterophylla. Our findings highlighted the significant role played by PGPR in medicinal plant yield and active ingredient accumulation when exposed to eCO2.

Novel Indigenous Strains and Communities with Copper Bioleaching Potential from the Amolanas Mine, Chile

Bioleaching, a process catalyzed by acidophilic microorganisms, offers a sustainable approach to metal extraction from sulfide minerals. Chalcopyrite, the world’s most abundant copper sulfide, presents challenges due to surface passivation limiting its bioleaching efficiency. Also, indigenous species and microbial communities may present high copper extraction rates and offer new possibilities for application in bioleaching processes. This study examines the bioleaching potential of microbial isolates and communities obtained from Amolanas Mine in Chile. Samples were collected, cultivated, and identified by Sanger sequencing. The bioleaching potential and biofilm formation of isolates and enrichments were evaluated on pyrite and chalcopyrite. The results show the isolation of nine Leptospirillum and two Acidithiobacillus strains. The bioleaching experiments demonstrated good copper bioleaching potentials of the Leptospirillum I2CS27 strain and EICA consortium (composed mainly of Leptospirillum ferriphilum, Acidiphilium sp., and Sulfobacillus thermosulfidooxidans), with 11% and 25% copper recovery rates, respectively. Microbial attachment to the surface mineral was not mandatory for increasing the bioleaching rates. Our findings underscore the importance of indigenous microbial communities in enhancing copper bioleaching efficiency.

Impact of the Biocontrol Product, Esquive® WP, on the Indigenous Grapevine Wood Microbiome after a 6-Year Application Period.

Grapevine trunk diseases (GTDs) are currently limiting grapevine productivity in many vineyards worldwide. As no chemical treatments are registered to control GTDs, biocontrol agents are being tested against these diseases. Esquive® WP, based on the fungus Trichoderma atroviride I-1237 strain, is the first biocontrol product registered in France to control GTDs. In this study, we determine whether, following grapevine pruning wound treatments with Esquive® WP, changes occurred or not in the indigenous microbial communities that are colonizing grapevine wood. Over a 6-year period, Esquive® WP was applied annually to pruning wounds on three grapevine cultivars located in three different regions. Wood samples were collected at 2 and 10 months after the Esquive® WP treatments. Based on MiSeq high-throughput sequencing analyses, the results showed that specific microbial communities were linked to each 'region/cultivar' pairing. In certain cases, a significant modification of alpha diversity indexes and the relative abundance of some microbial taxa were observed between treated and non-treated grapevines 2 months after Esquive® WP treatment. However, these modifications disappeared over time, i.e., 10 months post-treatment. This result clearly showed that Esquive® WP pruning wood treatment did not induce significant changes in the grapevine wood's microbiome, even after 6 years of recurrent applications on the plants.

The impact of lactic acid bacteria inoculation on the fermentation and metabolomic dynamics of indigenous Beijing douzhi microbial communities.

Douzhi, a traditional Chinese fermented beverage, features microbial communities primarily composed of lactic acid bacteria (LAB). As fermented foods continue to gain recognition and popularity, douzhi is attracting growing interest. However, investigation of the critical aspects of douzhi's fermentation processes, including fermentation characteristics and microbial community dynamics, remains vital for enhancing food safety and quality for douzhi, as well as for similar fermented food products. In this study, we collected douzhi microbial communities from four chain stores, using them as fermentation starter cultures. The microbial dynamics of the fermentation were analyzed, focusing on the inoculation of LAB strains and the transition from a mung bean-based matrix to skimmed milk. The metabolomic profiles of the fermented mung bean matrices were also studied. Douzhi samples obtained from representative chain stores were found to be overwhelmingly dominated by LAB. When inoculated along with the douzhi community, both LAB strains exhibited notable and substantial reductions in the pH value of the designated mung bean matrices compared to those inoculated indigenous microbiota. Specifically, Lactiplantibacillus plantarum CGMCC 1.1856 retained its population, whereas Pediococcus pentosaceus CGMCC 1.2695 exhibited a decrease in relative abundance. Using skimmed milk as a fermentation substrate instead of the mung bean matrix resulted in significant shifts in microbial communities, particularly leading to an increase in Escherichia sp. The metagenomic analyses and functional predictions illustrated that various metabolic functions were enhanced during the fermentation process due to LAB inoculation. The liquid chromatography-mass spectrometry based metabolomic analysis revealed that the inoculation of Lactiplantibacillus plantarum and Pediococcus pentosaceus in mung bean matrix did not introduce new metabolites but significantly altered the concentration and profile of existing metabolites, especially increased low molecular carbohydrates, which may enhance the nutritional potential of the fermented product. This study examines the microbial dynamics of douzhi microbiota fermentation, emphasizing the role of lactic acid bacteria in enhancing fermentation activity and metabolite profiles. These insights contribute to improving manufacturing processes and ensuring the safety and quality of douzhi and similar fermented foods.

Hydrocarbon Degradation and Biodegraders in Oil Spillage Sites in Port Harcourt

Information on remediation of soils polluted from the activities of artisanal crude oil refining is lacking. The functional capability of the indigenous microbial community and prospects for recovery of important bio-resources has also not been explored. The aim of this study was to identify the hydrocarbon biodegrader present in oil spillage sites in Port Harcourt. Samples were taken from various sites (labelled ss1, ss2, ss3 and controls) in Port Harcourt and the samples were transported to the lab for bacteriological assessment. The samples were cultured in Nutrient agar and Basal Salt Medium (BSM). The total heterotrophic bacteria counts were enumerated by serially diluting the fluid sample. Microbial characterization was done based on morphological, physiological and biochemical tests. From the results, Pseudomonas species and Bacillus species were the probable isolated from the culture of hydrocarbon contaminated environment. The results also revealed increased compared to the control organism that maintained the same growth level throughout the 5 days of incubation, the isolated bacteria (Pseudomonas species and Bacillus species) had steady bacterial growth. This study has shown that Bacillus species and Pseudomonas aeroginosa are potential agents of bioremediation of environmental hydrocarbon pollution.

Response Characteristics of the Community Structure and Metabolic Genes of Oil-Recovery Bacteria after Targeted Activation of Petroleum Hydrocarbon-Degrading Bacteria in Low-Permeability Oil Reservoirs.

The microbial enhanced oil recovery (MEOR) process has been identified as a promising alternative to conventional enhanced oil recovery methods because it is eco-friendly and economically advantageous. However, the knowledge about the composition and diversity of microbial communities in artificially regulated reservoirs, especially after activating petroleum hydrocarbon-degrading bacteria (PHDB) by injecting exogenous nutrients, is still insufficient. This study utilized a combination of high-throughput sequencing and metagenomics technology to reveal the structural evolution characteristics of the indigenous microbial community in the reservoir during the PHDB activated for enhanced oil recovery, as well as the response relationship between the expression of its oil production functional genes and crude oil biodegradation. Results showed that Pseudomonas (>75%) gradually evolves into a stable dominant microbial community in the reservoir during the activation of PHDB. Besides, the gene expression and KEGG pathways after crude oil undergoes biodegradation by PHDB show that the number of genes related to petroleum hydrocarbon metabolism dominates the metabolism (21.98%). Meanwhile, a preliminary schematic diagram was drawn to illustrate the evolution mechanism of the EOR metabolic pathway after the targeted activation of PHDB. Additionally, it was found that the abundance of hydrocarbon-degrading enzymes increased significantly, and the activity of alcohol dehydrogenase was higher than that of aldehyde dehydrogenase and monooxygenase after PHDB activation. These research results not only filled in and expanded the theoretical knowledge of MEOR based on artificial interference or regulation of reservoir oil-recovery functional microbial community structure but also provided guidance for the future application of MEOR technology in oil field operations.

Polymetallic contamination drives indigenous microbial community assembly dominated by stochastic processes at Pb-Zn smelting sites

Indigenous microbial communities in smelting areas are crucial for maintaining fragile ecosystem functions. However, the community assembly process and their responses to polymetallic pollution are poorly understood, especially the taxa in each bin from the amplicons that contributed to the assembly process. Herein, microbial diversity, co-occurrence patterns, assembly process and the intrinsic mechanisms across contamination gradients at a typical PbZn smelting site were systematically unravelled by high-throughput sequencing. The results showed a consistent compositional profile among the indigenous communities across sampling sites, wherein genera KD4–96 from Chloroflexi and Sphingomonas from Proteobacteria emerged as the most abundant taxa. Network modularity of the high- and middle-contaminated communities at Pb and Zn smelting sites was >0.44, indicating that community populations were clustered into modules to resist high heavy metal stress. Stochastic processes dominated the community assembly, with the greatest contribution from drift (DR), which was significantly correlated with Pb, Zn, Cr and Cu contents. What's particular was that the DR-controlled bins were dominated by Proteobacteria (typical r-strategists), while the HoS-controlled bins were by Chloroflexi (typical K-strategists). Furthermore, the proportion of DR in the bins dominated by Sphingomonadaceae (phylum Proteobacteria) increased gradually with the increase of heavy metal contents. These discoveries provide essential insights for community control in restoring and mitigating soil degradation at PbZn smelting sites.

Synthesis of iron-manganese bimetallic materials supported by activated carbon and application of activated persulfate in the degradation of soil contaminated by crude oil

Heterogeneous catalytic processes based on zero-valent iron (ZVI) have been developed to treat soil and wastewater pollutants. However, the agglomeration of ZVI reduces its ability to activate persulfate (PS). In this study, a new Fe–Mn@AC activated material was prepared to activated PS to treat oil-contaminated soil, and using the microscopic characterization of Fe–Mn@AC materials, the electron transfer mode during the Fe–Mn@AC activation of PS was clarified. Firstly, the petroluem degradation rate was optimized. When the PS addition amount was 8%, Fe–Mn@AC addition amount was 3% and the water to soil ratio was 3:1, the petroluem degradation rate in the soil reached to the maximum of 85.69% after 96 h of reaction. Then it was illustrated that sulfate and hydroxyl radicals played major roles in crude oil degradation, while singlet oxygen contributed slightly. Finally, the indigenous microbial community structures remaining after restoring the Fe–Mn@AC/PS systems were analyzed. The proportion of petroleum degrading bacteria in soil increased by 23% after oxidation by Fe–Mn@AC/PS system. Similarly, the germination rate of wheat seeds revealed that soil toxicity was greatly reduced after applying the Fe–Mn@AC/PS system. After the treatment with Fe–Mn@AC/PS system, the germination rate, root length and bud length of wheat seed were increased by 54.05%, 7.98 mm and 6.84 mm, respectively, compared with the polluted soil group. These results showed that the advanced oxidation system of Fe–Mn@AC activates PS and can be used in crude oil-contaminated soil remediation.

Silicon Fertilization Improves Sunflower Rhizosphere Microbial Community Structure and Reduces Parasitism by Orobanche cumana Wallr.

Sunflower broomrape (Orobanche cumana Wallr.) has severely restricted the development of the sunflower industry in China, and more efficient and convenient control methods are urgently needed. In this experiment, we investigated the effects of N, P and silica fertilizers on the parasitism rate of O. cumana, as well as on the yield of sunflower and native microbial communities in the field. Firstly, pot experiments were conducted to select the most effective fertilization method and to determine the physiological and biochemical indexes of sunflowers. Subsequently, field application studies were carried out to determine the physiological indexes, yield, O. cumana parasitism on sunflower, and the effect on the indigenous microbial community. The results demonstrate that compared with the CNP treatment (Control), the number of parasites under the N1P5 treatment significantly decreased by 66.15%. The exogenous application of silica can significantly reduce the number of O. cumana parasites. The treatments with N1P5 (N/P = 1:5) and available SiO2 content higher than 40 mg/kg (NS2, NS3, SF2 and SF3) significantly increased superoxide dismutase (SOD) activity and decreased malondialdehyde (MDA) content in sunflower leaves. In the field, fertilization significantly decreased the number of O. cumana parasites. The S treatment improved the native microbial community structure and enriched beneficial microorganisms, including Vicinamibacteria and Pyrinomonadaceae. Additionally, applying the S treatment significantly increased sunflower yield by 23.82% and crude protein content by 20.20%. In summary, the application of silicon fertilizer can effectively improve the host microbial community, reduce O. cumana parasitism and improve the yield and quality of sunflower.

Research on Microbial Community Structure in Different Blocks of Alkaline–Surfactant–Polymer Flooding to Confirm Optimal Stage of Indigenous Microbial Flooding

The microbial communities associated with alkaline–surfactant–polymer (ASP)-flooded reservoirs have rarely been investigated. In this study, high-throughput sequencing was used to analyse the indigenous microbial communities in two different blocks, the water flooding after the alkaline–surfactant–polymer flooding block and the alkaline–surfactant–polymer flooding block, and to ascertain the optimal stage for the implementation of indigenous microbial oil recovery technology. The different displacement blocks had significant effects on the indigenous microbial community at the genus level according to an alpha diversity analysis and community composition. In water flooding after alkaline–surfactant–polymer flooding, the dominant genus of Pseudomonas exceeded 30%, increasing to 52.1% in alkaline–surfactant–polymer flooding, but alpha diversity decreased. Through a co-occurrence network analysis, it was found that the complexity of the water flooding after alkaline–surfactant–polymer flooding was higher than that of alkaline–surfactant–polymer flooding. This means that the water flooding ecosystem after alkaline–surfactant–polymer flooding was more stable and less susceptible to external environmental influences. In addition, there were significant differences in the functional redundancy of microbial communities in different blocks. In summary, the optimal stage for implementing local microbial oil recovery technology may be water flooding after alkaline–surfactant–polymer flooding.

Interspecific barrier effect driven by heavy metals makes soil bacterial functional assembly more stochastic

Residual heavy metals in soils will destroy microbial community stability and influence its aggregation. However, exploring microbial ecology under heavy-metal stress still requires a conjoint analysis of bacterial interspecies communication and the community diversity maintenance mechanism. In this study, soil samples were collected from a heavy-metal-contaminated site in China to investigate the ecological response of indigenous microbial communities through high-throughput sequencing. Results showed that bacterial taxa and functions generated unusual decoupling phenomena. There were no significant differences in the diversity of species with the increase in concentration of heavy metals (Hg, Se, and Cr), but the functional diversity was lost. Also, the average niche breadth of bacterial species increased from 1.70 to 2.28, but community stability declined and the species assembly was always a deterministic process (NST <0.5). After the bacterial functional assembly changed from a stochastic process to a deterministic process (NST <0.5), it was transformed into a stochastic process (NST >0.5) again under the stress of high-concentration heavy metals, indicating that the collective stress resistance of bacterial communities changed from positive mutation into passive functional propagation. The research results can provide new insight into understanding the adaptive evolution of communities and ecosystem restoration under the stress of soil heavy metals.

Optimal conditions for nano-emulsified vegetable oil synthesis for the biostimulation of 1,1,2-trichloroethane and vinyl chloride contaminated groundwater in bioreactors

Contamination of groundwater with chlorinated aliphatic hydrocarbons (CAHs) has become increasingly widespread. Enhanced reductive dechlorination (ERD) by emulsified vegetable oil (EVO) is an environmentally friendly, low-carbon and sustainable technology that effectively eliminates the threat from CAHs. To improve the permeability and bioavailability of EVO in the low-permeability substratum, nano-emulsified vegetable oil (nanoEVO) can be synthesized using a modified phase inversion composition method (MPIC) by increasing the emulsification temperature that reduces the shear force required for the formation of nanodroplets and the interfacial tension between the mixed phase and water. The emulsification temperature of 60 °C, the water content of 40–70%, the droplet diameter (DD) of nanoEVO prepared by MPIC is ∼200 nm, and had good monodispersion (≤0.2). The high molecular weight and low solubility of vegetable oil, and similar size of droplet make nanoEVO remains homogeneous after storage for > one year. NanoEVO can effectively biostimulate indigenous bacteria in CAHs-contaminated groundwater to dechlorinate 1,1,2-trichloroethane (1,1,2-TCA) to ethene via vinyl chloride (VC). The maximum dihaloelimination rate of 1,1,2-TCA was ∼66.06 μM·Cl−·day−1 and the maximum hydrogenolysis rate of VC was ∼35.67 μM·Cl−·day−1. NanoEVO effectively increased the relative abundance of Dehalococcoides from <0.10 to 9.61%. The abundances of Dhc 16S rRNA gene and dehalogenase gene vcrA increased by 102 and 103, respectively. Biostimulation shaped the structure of microbial communities and promoted hydrolytic acidification and anaerobic fermentation. Moreover, the syntrophic VFA-oxidizing bacteria participated in secondary fermentation and were closely correlated with H2 consumption metabolism. By providing carbon sources and maintaining an anaerobic environment with stable pH and ORP, nanoEVO biostimulated the hydrolytic acidification led by fermentative bacteria, secondary fermentation with syntrophic VFA-oxidizing bacteria and reductive dechlorination carried out by dechlorinator, thus greatly increasing the CAH-dechlorinating ability of indigenous microbial communities.

Analyzing microbial communities and metabolic functions in estuaries affected by human activity to uncover bioelectrochemical system potential

In the context of bioelectrochemical systems (BES), a profound understanding of the taxonomic composition within indigenous microbial communities is crucial. Their metabolic versatility assumes a foundational role in dictating the functionality of BES, yielding diverse applications for bioenergy production and bioremediation in anthropogenically impacted estuaries. Employing high-throughput sequencing of the V3-V4 region of 16S rRNA and predictive metagenomic analyses of three different estuaries samples (eutrophicated urban reservoir, mud volcano impacted river, and its river mouth), this study delves into the intricate interplay between these communities and their metabolic functions in response to human-induced perturbations, with a specific focus on their applicability to BES. Our findings illuminate remarkable distinctions among the three samples, manifesting in variations in microbial composition and functional metabolic pathways within the respective ecosystems. The mud volcano-affected river, characterized by the highest microbial diversity, exhibited the most diverse array of functional metabolic processes, prominently dominated by chemoheterotrophy (67.43%). In contrast, the river mouth displayed a distinct penchant for autotrophy (33.33%). The eutrophicated urban reservoir showcased a balanced coexistence of chemoheterotrophy (41.18%) and autotrophy (35.29%). Regarding metabolic potential for BES application, most of metabolism potential were associated with anodic activity, while cathodic activity was restricted to autotrophy and its relatives. The results suggested that the microbial communities anthropogenically impacted estuaries were potentially used for anodic and cathodic reactions in BES as electrogens to generate bioelectricity and reduce of pollutants.

Investigating the activity of indigenous microbial communities from Italian depleted gas reservoirs and their possible impact on underground hydrogen storage.

H2 produced from renewable energies will play a central role in both greenhouse gas reduction and decarbonization by 2050. Nonetheless, to improve H2 diffusion and utilization as a fuel, large storage capacity systems are needed. Underground storage of natural gas in depleted reservoirs, aquifers and salt caverns is a well-established technology. However, new challenges arise when it comes to storing hydrogen due to the occurrence and activity of indigenous microbial populations in deep geological formations. In a previous study, four Italian natural gas reservoirs were characterized both from a hydro-chemical and microbiological point of view, and predictive functional analyses were carried out with the perspective of underground hydrogen storage (UHS). In the present work, formation waters from the same reservoirs were used as inoculant during batch cultivation tests to characterize microbial activity and its effects on different gas mixtures. Results evidence a predominant acidogenic/acetogenic activity, whilst methanogenic and sulfate reducing activity were only marginal for all tested inoculants. Furthermore, the microbial activation of tested samples is strongly influenced by nutrient availability. Obtained results were fitted and screened in a computational model which would allow deep insights in the study of microbial activity in the context of UHS.

The effect of anaerobic digestate as an organic soil fertilizer on the diversity and structure of the indigenous soil microbial and nematode communities.

Anaerobic digestate is a popular soil additive which can promote sustainability and transition toward a circular economy. This study addresses how anaerobic digestate modifies soil health when combined with a common chemical fertilizer. Attention was given to soil microbes and, a neglected but of paramount importance soil taxonomic group, soil nematodes. A mesocosm experiment was set up in order to assess the soil's microbial and nematode community. The results demonstrated that the microbial diversity was not affected by the different fertilization regimes, although species richness increased after digestate and mixed fertilization. The composition and abundance of nematode community did not respond to any treatment. Mixed fertilization notably increased potassium (K) and boron (B) levels, while nitrate (NO3-) levels were uniformly elevated across fertilized soils, despite variations in nitrogen input. Network analysis revealed that chemical fertilization led to a densely interconnected network with mainly mutualistic relationships which could cause ecosystem disruption, while digestate application formed a more complex community based on bacterial interactions. However, the combination of both orchestrated a more balanced and less complex community structure, which is more resilient to random disturbances, but on the downside, it is more likely to collapse under targeted perturbations.