Transcriptome-Stable Isotope Probing Provides Targeted Functional and Taxonomic Insights Into Microaerobic Pollutant-Degrading Aquifer Microbiota

Systematic evaluation of the impact of standard storage conditions on plasmid conjugation behavior in wastewater samples

Filter mating experiment is widely used to study the conjugation behavior of plasmids and associated antibiotic resistance in environmental settings, however, the influence and biases brought by sample storage conditions (temperature and duration) were not yet systematically elaborated. This study systematically investigated the influence of standard storage conditions (4 °C, -20 °C, -80 °C) on plasmid conjugation behavior in influent (Inf) and activated sludge (AS) samples from sewage treatment plants (STP). The findings revealed a significant reduction in conjugation efficiency under all the tested storage conditions except for 1-week storage at 4 °C. Notably, storing at -80 °C maintained conjugation activities in activated sludge more effectively compared to -20 °C. However, the preservation performance was less effective for influent samples, which consist mainly of anaerobe-dominant communities. Systematic loss of IncH-type plasmids was observed in influent samples stored at 4 °C and -20 °C. Correspondingly, the plasmid-carrying resistome genotypes detected in the influent samples showed a clear downward trend with the increase in storage duration when stored at 4 °C and -20 °C. A relatively uniform composition in terms of incompatibility type and resistome profile was observed across activated sludge samples, regardless of the varied storage conditions. This study highlights the critical impact of storage conditions on plasmid conjugation behavior and resistome composition, offering valuable insights for optimal sample handling in resistome research.

Advances and perspectives of using stable isotope probing (SIP)-based technologies in contaminant biodegradation

Stable isotope probing (SIP) is a powerful tool to study microbial community structure and function in both nature and engineered environments. Coupling with advanced genomics and other techniques, SIP studies have generated substantial information to allow researchers to draw a clearer picture of what is occurring in complex microbial ecosystems. This review provides an overview of the advances of SIP-based technologies over time, summarizes the status of SIP applications to contaminant biodegradation, provides critical perspectives on ecological interactions within the community, and important factors (controllable and non-controllable) to be considered in SIP experimental designs and data interpretation. Current trend and perspectives of adapting SIP techniques for environmental applications are also discussed.

DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms

Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of ¹³C, ¹⁸O, or ¹⁵N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labelled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labelled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labelling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, or even metagenomes and metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labelled microorganisms. Analysis of labelled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allowed using labelled substrates at environmentally relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter, we provide protocols for obtaining labelled DNA, RNA, and proteins that can be used for downstream omics-based analyses.

Depth-resolved microbial diversity and functional profiles of trichloroethylene-contaminated soils for Biolog EcoPlate-based biostimulation strategy

This study explores the toxic effect of TCE at different depths of sub-surface soil and underpins microbial community-level suitable carbon (C)-sources that provided directionality to the in situ biostimulation effort via augmentation strategy for effective TCE remediation in soil. The impacts on resident microbial communities and their functional profiles that govern the TCE biodegradation process were identified. Highly contaminated PW01 soil (9 m depth) had severely limited microbial diversity and was enriched in Proteobacteria and Firmicutes. The abundance of TCE degradation-associated genera was observed in all contaminated samples, and the abundance of TCE-degradation-related taxa were positively correlated with soil TCE contamination levels. Community-level metabolic activity associated with the utilization of diverse external C-sources was directly influenced by TCE concentration and soil depth. Multivariate data analysis revealed that the functional genus, TCE concentration, and selected available C substrate uptake capacity correlated in soil samples. Pearson's correlation tests revealed that C sources such as L-arginine, phenylethylamine and γ-hydroxybutyric acid utilization trait exhibited significant positive correlations with chloroalkane and chloroalkene degradation pathway abundance. Ultimately, depth and TCE contamination level-associated soil microbiota and their most preferred C-source understanding could add to facilitate effective biostimulation via external nutrient amendment for efficient in situ TCE degradation.

The Influence of Kerosene on Microbiomes of Diverse Soils

One of the most important challenges for soil science is to determine the limits for the sustainable functioning of contaminated ecosystems. The response of soil microbiomes to kerosene pollution is still poorly understood. Here, we model the impact of kerosene leakage on the composition of the topsoil microbiome in pot and field experiments with different loads of added kerosene (loads up to 100 g/kg; retention time up to 360 days). At four time points we measured kerosene concentration and sequenced variable regions of 16S ribosomal RNA in the microbial communities. Mainly alkaline Dystric Arenosols with low content of available phosphorus and soil organic matter had an increased fraction of Actinobacteriota, Firmicutes, Nitrospirota, Planctomycetota, and, to a lesser extent, Acidobacteriota and Verrucomicobacteriota. In contrast, in highly acidic Fibric Histosols, rich in soil organic matter and available phosphorus, the fraction of Acidobacteriota was higher, while the fraction of Actinobacteriota was lower. Albic Luvisols occupied an intermediate position in terms of both physicochemical properties and microbiome composition. The microbiomes of different soils show similar response to equal kerosene loads. In highly contaminated soils, the proportion of anaerobic bacteria-metabolizing hydrocarbons increased, whereas the proportion of aerobic bacteria decreased. During the field experiment, the soil microbiome recovered much faster than in the pot experiments, possibly due to migration of microorganisms from the polluted area. The microbial community of Fibric Histosols recovered in 6 months after kerosene had been loaded, while microbiomes of Dystric Arenosols and Albic Luvisols did not restore even after a year.

Methodological Advances to Study Contaminant Biotransformation: New Prospects for Understanding and Reducing Environmental Persistence?

Complex microbial communities in environmental systems play a key role in the detoxification of chemical contaminants by transforming them into less active metabolites or by complete mineralization. Biotransformation, i.e., transformation by microbes, is well understood for a number of priority pollutants, but a similar level of understanding is lacking for many emerging contaminants encountered at low concentrations and in complex mixtures across natural and engineered systems. Any advanced approaches aiming to reduce environmental exposure to such contaminants (e.g., novel engineered biological water treatment systems, design of readily degradable chemicals, or improved regulatory assessment strategies to determine contaminant persistence a priori) will depend on understanding the causal links among contaminant removal, the key driving agents of biotransformation at low concentrations (i.e., relevant microbes and their metabolic activities), and how their presence and activity depend on environmental conditions. In this Perspective, we present the current understanding and recent methodological advances that can help to identify such links, even in complex environmental microbiomes and for contaminants present at low concentrations in complex chemical mixtures. We discuss the ensuing insights into contaminant biotransformation across varying environments and conditions and ask how much closer we have come to designing improved approaches to reducing environmental exposure to contaminants.

Dechloromonas and close relatives prevail during hydrogenotrophic denitrification in stimulated microcosms with oxic aquifer material

Globally occurring nitrate pollution in groundwater is harming the environment and human health. In situ hydrogen addition to stimulate denitrification has been proposed as a remediation strategy. However, observed nitrite accumulation and incomplete denitrification are severe drawbacks that possibly stem from the specific microbial community composition. We set up a microcosm experiment comprising sediment and groundwater from a nitrate polluted oxic oligotrophic aquifer. After the microcosms were sparged with hydrogen gas, samples were taken regularly within 122 h for nitrate and nitrite measurements, community composition analysis via 16S rRNA gene amplicon sequencing and gene and transcript quantification via qPCR of reductase genes essential for complete denitrification. The highest nitrate reduction rates and greatest increase in bacterial abundance coincided with a 15.3-fold increase in relative abundance of Rhodocyclaceae, specifically six ASVs that are closely related to the genus Dechloromonas. The denitrification reductase genes napA, nirS and clade I nosZ also increased significantly over the observation period. We conclude that taxa of the genus Dechloromonas are the prevailing hydrogenotrophic denitrifiers in this nitrate polluted aquifer and the ability of hydrogenotrophic denitrification under the given conditions is species-specific.

Assessing Biodegradability of Chemical Compounds from Microbial Community Growth Using Flow Cytometry

Compound biodegradability tests with natural microbial communities form an important keystone in the ecological assessment of chemicals. However, biodegradability tests are frequently limited by a singular focus either on the chemical and potential transformation products or on the individual microbial species degrading the compound. Here, we investigated a methodology to simultaneously analyze community compositional changes and biomass growth on dosed test compound from flow cytometry (FCM) data coupled to machine-learned cell type recognition. We quantified the growth of freshwater microbial communities on a range of carbon dosages of three readily biodegradable reference compounds, phenol, 1-octanol, and benzoate, in comparison to three fragrances, methyl jasmonate, myrcene, and musk xylene (as a nonbiodegradable control). Compound mass balances with between 0.1 to 10 mg C · liter-1 phenol or 1-octanol, inferred from cell numbers, parent compound analysis, and CO2 evolution, as well as use of 14C-labeled compounds, showed between 6 and 25% mg C · mg C-1 substrate incorporation into biomass within 2 to 4 days and 25 to 45% released as CO2 In contrast, similar dosage of methyl jasmonate and myrcene supported slower (4 to 10 days) and less (2.6 to 6.6% mg C · mg C-1 with 4.9 to 22% CO2) community growth. Community compositions inferred from machine-learned cell type recognition and 16S rRNA amplicon sequencing showed substrate- and concentration-dependent changes, with visible enrichment of microbial subgroups already at 0.1 mg C · liter-1 phenol and 1-octanol. In general, community compositions were similar at the start and after the stationary phase of the microbial growth, except at the highest used substrate concentrations of 100 to 1,000 mg C · liter-1 Flow cytometry cell counting coupled to deconvolution of communities into subgroups is thus suitable to infer biodegradability of organic chemicals, permitting biomass balances and near-real-time assessment of relevant subgroup changes.IMPORTANCE The manifold effects of potentially toxic compounds on microbial communities are often difficult to discern. Some compounds may be transformed or completely degraded by few or multiple strains in the community, whereas others may present inhibitory effects. In this study, we benchmark a new method based on machine-learned microbial cell recognition to rapidly follow dynamic changes in aquatic communities. We further determine productive biodegradation upon dosing of a number of well-known readily biodegradable tester compounds at a variety of concentrations. Microbial community growth was quantified using flow cytometry, and the multiple cell parameters measured were used in parallel to deconvolute the community on the basis of similarity to previously standardized cell types. Biodegradation was further confirmed by chemical analysis, showing how distinct changes in specific populations correlate to degradation. The method holds great promise for near-real-time community composition changes and deduction of compound biodegradation in natural microbial communities.

Availability of Nitrite and Nitrate as Electron Acceptors Modulates Anaerobic Toluene-Degrading Communities in Aquifer Sediments

Microorganisms are essential in the degradation of environmental pollutants. Aromatic hydrocarbons, e.g., benzene, toluene, ethylbenzene, and xylene (BTEX), are common aquifer contaminants, whose degradation in situ is often limited by the availability of electron acceptors. It is clear that different electron acceptors such as nitrate, iron, or sulfate support the activity of distinct degraders. However, this has not been demonstrated for the availability of nitrate vs. nitrite, both of which can be respired in reductive nitrogen cycling. Here via DNA-stable isotope probing, we report that nitrate and nitrite provided as electron acceptors in different concentrations and ratios not only modulated the microbial communities responsible for toluene degradation but also influenced how nitrate reduction proceeded. Zoogloeaceae members, mainly Azoarcus spp., were the key toluene degraders with nitrate-only, or both nitrate and nitrite as electron acceptors. In addition, a shift within Azoarcus degrader populations was observed on the amplicon sequence variant (ASV) level depending on electron acceptor ratios. In contrast, members of the Sphingomonadales were likely the most active toluene degraders when only nitrite was provided. Nitrate reduction did not proceed beyond nitrite in the nitrate-only treatment, while it continued when nitrite was initially also present in the microcosms. Likely, this was attributed to the fact that different microbial communities were stimulated and active in different microcosms. Together, these findings demonstrate that the availability of nitrate and nitrite can define degrader community selection and N-reduction outcomes. It also implies that nitrate usage efficiency in bioremediation could possibly be enhanced by an initial co-supply of nitrite, via modulating the active degrader communities.

Microbial Degradation of Hydrocarbons-Basic Principles for Bioremediation: A Review

Crude oil-derived hydrocarbons constitute the largest group of environmental pollutants worldwide. The number of reports concerning their toxicity and emphasizing the ultimate need to remove them from marine and soil environments confirms the unceasing interest of scientists in this field. Among the various techniques used for clean-up actions, bioremediation seems to be the most acceptable and economically justified. Analysis of recent reports regarding unsuccessful bioremediation attempts indicates that there is a need to highlight the fundamental aspects of hydrocarbon microbiology in a clear and concise manner. Therefore, in this review, we would like to elucidate some crucial, but often overlooked, factors. First, the formation of crude oil and abundance of naturally occurring hydrocarbons is presented and compared with bacterial ability to not only survive but also to utilize such compounds as an attractive energy source. Then, the significance of nutrient limitation on biomass growth is underlined on the example of a specially designed experiment and discussed in context of bioremediation efficiency. Next, the formation of aerobic and anaerobic conditions, as well as the role of surfactants for maintaining appropriate C:N:P ratio during initial stages of biodegradation is explained. Finally, a summary of recent scientific reports focused on the removal of hydrocarbon contaminants using bioaugmentation, biostimulation and introduction of surfactants, as well as biosurfactants, is presented. This review was designed to be a comprehensive source of knowledge regarding the unique aspects of hydrocarbon microbiology that may be useful for planning future biodegradation experiments. In addition, it is a starting point for wider debate regarding the limitations and possible improvements of currently employed bioremediation strategies.

Microaerobic conditions caused the overwhelming dominance of Acinetobacter spp. and the marginalization of Rhodococcus spp. in diesel fuel/crude oil mixture-amended enrichment cultures

The aim of the present study was to reveal how different microbial communities evolve in diesel fuel/crude oil-contaminated environments under aerobic and microaerobic conditions. To investigate this question, aerobic and microaerobic bacterial enrichments amended with a diesel fuel/crude oil mixture were established and analysed. The representative aerobic enrichment community was dominated by Gammaproteobacteria (64.5%) with high an abundance of Betaproteobacteriales (36.5%), followed by Alphaproteobacteria (8.7%), Actinobacteria (5.6%), and Candidatus Saccharibacteria (4.5%). The most abundant alkane monooxygenase (alkB) genotypes in this enrichment could be linked to members of the genus Rhodococcus and to a novel Gammaproteobacterium, for which we generated a high-quality draft genome using genome-resolved metagenomics of the enrichment culture. Contrarily, in the microaerobic enrichment, Gammaproteobacteria (99%) overwhelmingly dominated the microbial community with a high abundance of the genera Acinetobacter (66.3%), Pseudomonas (11%) and Acidovorax (11%). Under microaerobic conditions, the vast majority of alkB gene sequences could be linked to Pseudomonas veronii. Consequently, results shed light on the fact that the excellent aliphatic hydrocarbon degrading Rhodococcus species favour clear aerobic conditions, while oxygen-limited conditions can facilitate the high abundance of Acinetobacter species in aliphatic hydrocarbon-contaminated subsurface environments.

Genome analysis provides insights into microaerobic toluene-degradation pathway of Zoogloea oleivorans BucT

Zoogloea oleivorans, capable of using toluene as a sole source of carbon and energy, was earlier found to be an active degrader under microaerobic conditions in aquifer samples. To uncover the genetic background of the ability of microaerobic toluene degradation in Z. oleivorans, the whole-genome sequence of the type strain Buc^T was revealed. Metatranscriptomic sequence reads, originated from a previous SIP study on microaerobic toluene degradation, were mapped on the genome. The genome (5.68 Mb) had a mean G + C content of 62.5%, 5005 protein coding gene sequences and 80 RNA genes. Annotation predicted that 66 genes were involved in the metabolism of aromatic compounds. Genome analysis revealed the presence of a cluster with genes coding for a multicomponent phenol-hydroxylase system and a complete catechol meta-cleavage pathway. Another cluster flanked by mobile-element protein coding genes coded a partial catechol meta-cleavage pathway including a subfamily I.2.C-type extradiol dioxygenase. Analysis of metatranscriptomic data of a microaerobic toluene-degrading enrichment, containing Z .  oleivorans as an active-toluene degrader revealed that a toluene dioxygenase-like enzyme was responsible for the ring-hydroxylation, while enzymes of the partial catechol meta-cleavage pathway coding cluster were responsible for further degradation of the aromatic ring under microaerobic conditions. This further advances our understanding of aromatic hydrocarbon degradation between fully oxic and strictly anoxic conditions.

Nitric Oxide Dismutase (nod) Genes as a Functional Marker for the Diversity and Phylogeny of Methane-Driven Oxygenic Denitrifiers

Oxygenic denitrification represents a new route in reductive nitrogen turnover which differs from canonical denitrification in how nitric oxide (NO) is transformed into dinitrogen gas. Instead of NO reduction via N₂O to N₂, NO is proposed to be directly disproportionated into N₂ and O₂ in oxygenic denitrification, catalyzed by the putative NO dismutase (Nod). Although a high diversity of nod genes has been recovered from various environments, still little is known about the niche partitioning and ecophysiology of oxygenic denitrifiers. One constraint is that nod as a functional marker for oxygenic denitrifiers is not well established. To address this issue, we compared the diversity and phylogeny of nod, 16S rRNA and pmoA gene sequences of four NC10 enrichments that are capable of methane-driven oxygenic denitrification and one environmental sample. The phylogenies of nod, 16S rRNA and pmoA genes of these cultures were generally congruent. The diversity of NC10 bacteria inferred from different genes was also similar in each sample. A new set of NC10-specific nod primers was developed and used in qPCR. The abundance of NC10 bacteria inferred from nod genes was constantly lower than via 16S rRNA genes, but the difference was within one order of magnitude. These results suggest that nod is a suitable molecular marker for studying the diversity and phylogeny of methane-driven oxygenic denitrifiers, the further investigation of which may be of value to develop enhanced strategies for sustainable nitrogen or methane removal.

Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing

Metatranscriptomics is a powerful tool for capturing gene expression patterns in microbial communities and investigating their responses to environmental conditions. Stable isotope probing (SIP) is a method to target specific functional groups of microorganisms in environmental samples. The combination of RNA-SIP with metatranscriptomic analysis enhances the detection and identification of mRNA from target microorganisms. In this chapter we provide a protocol for RNA-SIP, mRNA enrichment, and mRNA preparation for high-throughput sequencing using an example of targeting methanotrophs in rice field soil.

RNA Stable Isotope Probing (RNA-SIP)

Stable isotope probing is a combined molecular and isotopic technique used to probe the identity and function of uncultivated microorganisms within environmental samples. Employing stable isotopes of common elements such as carbon and nitrogen, RNA-SIP exploits an increase in the buoyant density of RNA caused by the active metabolism and incorporation of heavier mass isotopes into the RNA after cellular utilization of labeled substrates pulsed into the community. Labeled RNAs are subsequently separated from unlabeled RNAs by density gradient centrifugation followed by identification of the RNAs by sequencing. Therefore, RNA stable isotope probing is a culture-independent technique that provides simultaneous information about microbiome community, composition and function. This chapter presents the detailed protocol for performing an RNA-SIP experiment, including the formation, ultracentrifugation, and fractional analyses of stable isotope-labeled RNAs extracted from environmental samples.