Microplastic ingestion affects hydrogen production and microbiomes in the gut of the terrestrial isopod Porcellio scaber.

Microplastic (MP) is an environmental burden and enters food webs via ingestion by macrofauna, including isopods (Porcellio scaber) in terrestrial ecosystems. Isopods represent ubiquitously abundant, ecologically important detritivores. However, MP-polymer specific effects on the host and its gut microbiota are unknown. We tested the hypothesis that biodegradable (polylactic acid [PLA]) and non-biodegradable (polyethylene terephthalate [PET]; polystyrene [PS]) MPs have contrasting effects on P. scaber mediated by changes of the gut microbiota. The isopod fitness after an 8-week MP-exposure was generally unaffected, although the isopods showed avoidance behaviour to PS-food. MP-polymer specific effects on gut microbes were detected, including a stimulation of microbial activity by PLA compared with MP-free controls. PLA stimulated hydrogen emission from isopod guts, while PET and PS were inhibitory. We roughly estimated 107 kg year-1 hydrogen emitted from the isopods globally and identified their guts as anoxic, significant mobile sources of reductant for soil microbes despite the absence of classical obligate anaerobes, likely due to Enterobacteriaceae-related fermentation activities that were stimulated by lactate generated during PLA-degradation. The findings suggest negative effects of PET and PS on gut fermentation, modulation of important isopod hydrogen emissions by MP pollution and the potential of MP to affect terrestrial food webs.

Intermediate Levels of Predation and Nutrient Enrichment Enhance the Activity of Ibuprofen-Degrading Bacteria.

Water is the most indispensable natural resource; yet, organic pollution of freshwater sources is widespread. In recent years, there has been increasing concern over the vast array of emerging organic contaminants (EOCs) in the effluent of wastewater treatment plants (WWTPs). Several of these EOCs are degraded within the pore space of riverbeds by active microbial consortia. However, the mechanisms behind this ecosystem service are largely unknown. Here, we report how phosphate concentration and predator-prey interactions drive the capacity of bacteria to process a model EOC (ibuprofen). The presence of phosphate had a significant positive effect on the population growth rate of an ibuprofen-degrading strain. Thus, when phosphate was present, ibuprofen removal efficiency increased. Moreover, low and medium levels of predation, by a ciliated protozoan, stimulated bacterial population growth. This unimodal effect of predation was lost under high phosphate concentration, resulting in the flattening of the relationships between predator density and population growth of ibuprofen degraders. Our results suggest that moderate nutrient and predation levels promote the growth rate of bacterial degraders and, consequently, the self-purifying capability of the system. These findings enhance our understanding of the mechanisms by which riverbed communities drive the processing of EOCs.

Microplastic polymer properties as deterministic factors driving terrestrial plastisphere microbiome assembly and succession in the field.

Environmental microplastic (MP) is ubiquitous in aquatic and terrestrial ecosystems providing artificial habitats for microbes. Mechanisms of MP colonization, MP polymer impacts, and effects on soil microbiomes are largely unknown in terrestrial systems. Therefore, we experimentally tested the hypothesis that MP polymer type is an important deterministic factor affecting MP community assembly by incubating common MP polymer types in situ in landfill soil for 14 months. 16S rRNA gene amplicon sequencing indicated that MP polymers have specific impacts on plastisphere microbiomes, which are subsets of the soil microbiome. Chloroflexota, Gammaproteobacteria, certain Nitrososphaerota, and Nanoarchaeota explained differences among MP polymers and time points. Plastisphere microbial community composition derived from different MP diverged over time and was enriched in potential pathogens. PICRUSt predictions of pathway abundances and quantitative PCR of functional marker genes indicated that MP polymers exerted an ambivalent effect on genetic potentials of biogeochemical cycles. Overall, the data indicate that (i) polymer type as deterministic factor rather than stochastic factors drives plastisphere community assembly, (ii) MP impacts greenhouse gas metabolism, xenobiotic degradation and pathogen distribution, and (iii) MP serves as an ideal model system for studying fundamental questions in microbial ecology such as community assembly mechanisms in terrestrial environments.

Genomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov.

Three strains (H4-D09T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate-formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus. Core genome phylogeny of the type strain H4-D09T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C18 : 1ω7c, C19 : 0cyclo ω7c, and C16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L).On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus, for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09T=LMG 31941T= DSM 111585T) is proposed.

Aerobic Methanotrophy and Co-occurrence Networks of a Tropical Rainforest and Oil Palm Plantations in Malaysia.

Oil palm (OP) plantations are gradually replacing tropical rainforest in Malaysia, one of the largest palm oil producers globally. Conversion of lands to OP plantations has been associated with compositional shifts of the microbial community, with consequences on the greenhouse gas (GHG) emissions. While the impact of the change in land use has recently been investigated for microorganisms involved in N2O emission, the response of the aerobic methanotrophs to OP agriculture remains to be determined. Here, we monitored the bacterial community composition, focusing on the aerobic methanotrophs, in OP agricultural soils since 2012, 2006, and 1993, as well as in a tropical rainforest, in 2019 and 2020. High-affinity methane uptake was confirmed, showing significantly lower rates in the OP plantations than in the tropical rainforest, but values increased with continuous OP agriculture. The bacterial, including the methanotrophic community composition, was modified with ongoing OP agriculture. The methanotrophic community composition was predominantly composed of unclassified methanotrophs, with the canonical (Methylocystis) and putative methanotrophs thought to catalyze high-affinity methane oxidation present at higher relative abundance in the oldest OP plantation. Results suggest that the methanotrophic community was relatively more stable within each site, exhibiting less temporal variations than the total bacterial community. Uncharacteristically, a 16S rRNA gene-based co-occurrence network analysis revealed a more complex and connected community in the OP agricultural soil, which may influence the resilience of the bacterial community to disturbances. Overall, we provide a first insight into the ecology and role of the aerobic methanotrophs as a methane sink in OP agricultural soils.

Recovery in methanotrophic activity does not reflect on the methane-driven interaction network after peat mining.

Aerobic methanotrophs are crucial in ombrotrophic peatlands, driving the methane and nitrogen cycles. Peat mining adversely affects the methanotrophs, but activity and community composition/abundances may recover after restoration. Considering that the methanotrophic activity and growth are significantly stimulated in the presence of other microorganisms, the methane-driven interaction network, encompassing methanotrophs and non-methanotrophs (i.e., methanotrophic interactome), may also be relevant in conferring community resilience. Yet, little is known of the response and recovery of the methanotrophic interactome to disturbances. Here, we determined the recovery of the methanotrophic interactome as inferred by a co-occurrence network analysis, comparing a pristine and restored peatland. We coupled a DNA-based stable isotope probing (SIP) approach using 13C-CH4 to a co-occurrence network analysis derived from the 13C-enriched 16S rRNA gene sequences to relate the response in methanotrophic activity to the structuring of the interaction network. Methanotrophic activity and abundances recovered after peat restoration since 2000. 'Methylomonaceae' was the predominantly active methanotrophs in both peatlands, but differed in the relative abundance of Methylacidiphilaceae and Methylocystis However, bacterial community composition was distinct in both peatlands. Likewise, the methanotrophic interactome was profoundly altered in the restored peatland. Structuring of the interaction network after peat mining resulted in the loss of complexity and modularity, indicating a less connected and efficient network, which may have consequences in the event of recurring/future disturbances. Therefore, determining the response of the methane-driven interaction network, in addition to relating methanotrophic activity to community composition/abundances, provided a more comprehensive understanding of the resilience of the methanotrophs.Importance The resilience and recovery of microorganisms from disturbances are often determined with regard to their activity and community composition/abundances. Rarely has the response of the network of interacting microorganisms been considered, despite accumulating evidence showing that microbial interaction modulates community functioning. Comparing the methane-driven interaction network of a pristine and restored peatland, our findings revealed that the metabolically active microorganisms were less connected and formed less modular 'hubs' in the restored peatland, indicative of a less complex network which may have consequences with recurring disturbances and environmental changes. This also suggests that the resilience and full recovery in the methanotrophic activity and abundances do not reflect on the interaction network. Therefore, it is relevant to consider the interaction-induced response, in addition to documenting changes in activity and community composition/abundances, to provide a comprehensive understanding of the resilience of microorganisms to disturbances.

Pseudomonas campi sp. nov., a nitrate-reducing bacterium isolated from grassland soil.

A novel strain was isolated from grassland soil that has the potential to assimilate ammonium by the reduction of nitrate in the presence of oxygen. Whole genome sequence analysis revealed the presence of an assimilatory cytoplasmic nitrate reductase gene nasA and the assimilatory nitrite reductase genes nirBD which are involved in the sequential reduction of nitrate to nitrite and further to ammonium, respectively. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the isolate represents a member of the genus Pseudomonas. The closest phylogenetic neighbours based on 16S rRNA gene sequence analysis are the type strains of Pseudomonas peli (98.17%) and Pseudomonas guineae (98.03%). In contrast, phylogenomic analysis revealed a close relationship to Pseudomonas alcaligenes. Computation of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours of S1-A32-2T revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics. On the basis of these results, it was concluded that the soil isolate represents a novel species of the genus Pseudomonas, for which the name Pseudomonas campi sp. nov. (type strain S1-A32-2T=LMG 31521T=DSM 110222T) is proposed.

Biodegradation of metoprolol in oxic and anoxic hyporheic zone sediments: unexpected effects on microbial communities.

Metoprolol is widely used as a beta-blocker and considered an emerging contaminant of environmental concern due to pseudo persistence in wastewater effluents that poses a potential ecotoxicological threat to aquatic ecosystems. Microbial removal of metoprolol in the redox-delineated hyporheic zone (HZ) was investigated using streambed sediments supplemented with 15 or 150 µM metoprolol in a laboratory microcosm incubation under oxic and anoxic conditions. Metoprolol disappeared from the aqueous phase under oxic and anoxic conditions within 65 and 72 days, respectively. Metoprolol was refed twice after initial depletion resulting in accelerated disappearance under both conditions. Metoprolol disappearance was marginal in sterile control microcosms with autoclaved sediment. Metoprolol was transformed mainly to metoprolol acid in oxic microcosms, while metoprolol acid and α-hydroxymetoprolol were formed in anoxic microcosms. Transformation products were transient and disappeared within 30 days under both conditions. Effects of metoprolol on the HZ bacterial community were evaluated using DNA- and RNA-based time-resolved amplicon Illumina MiSeq sequencing targeting the 16S rRNA gene and 16S rRNA, respectively, and were prominent on 16S rRNA rather than 16S rRNA gene level suggesting moderate metoprolol-induced activity-level changes. A positive impact of metoprolol on Sphingomonadaceae and Enterobacteriaceae under oxic and anoxic conditions, respectively, was observed. Nitrifiers were impaired by metoprolol under oxic and anoxic conditions. Collectively, our findings revealed high metoprolol biodegradation potentials in the hyporheic zone under contrasting redox conditions associated with changes in the active microbial communities, thus contributing to the attenuation of micropollutants. KEY POINTS: • High biotic oxic and anoxic metoprolol degradation potentials in the hyporheic zone. • Key metoprolol-associated taxa included Sphingomonadaceae, Enterobacteraceae, and Promicromonosporaceae. • Negative impact of metoprolol on nitrifiers.

Bacterial Diversity Controls Transformation of Wastewater-Derived Organic Contaminants in River-Simulating Flumes.

Hyporheic zones are the water-saturated flow-through subsurfaces of rivers which are characterized by the simultaneous occurrence of multiple physical, biological, and chemical processes. Two factors playing a role in the hyporheic attenuation of organic contaminants are sediment bedforms (a major driver of hyporheic exchange) and the composition of the sediment microbial community. How these factors act on the diverse range of organic contaminants encountered downstream from wastewater treatment plants is not well understood. To address this knowledge gap, we investigated dissipation half-lives (DT50s) of 31 substances (mainly pharmaceuticals) under different combinations of bacterial diversity and bedform-induced hyporheic flow using 20 recirculating flumes in a central composite face factorial design. By combining small-volume pore water sampling, targeted analysis, and suspect screening, along with quantitative real-time PCR and time-resolved amplicon Illumina MiSeq sequencing, we determined a comprehensive set of DT50s, associated bacterial communities, and microbial transformation products. The resulting DT50s of parent compounds ranged from 0.5 (fluoxetine) to 306 days (carbamazepine), with 20 substances responding significantly to bacterial diversity and four to both diversity and hyporheic flow. Bacterial taxa that were associated with biodegradation included Acidobacteria (groups 6, 17, and 22), Actinobacteria (Nocardioides and Illumatobacter), Bacteroidetes (Terrimonas and Flavobacterium) and diverse Proteobacteria (Pseudomonadaceae, Sphingomonadaceae, and Xanthomonadaceae). Notable were the formation of valsartan acid from irbesartan and valsartan, the persistence of N-desmethylvenlafaxine across all treatments, and the identification of biuret as a novel transformation product of metformin. Twelve additional target transformation products were identified, which were persistent in either pore or surface water of at least one treatment, indicating their environmental relevance.

Copper in Wood Preservatives Delayed Wood Decomposition and Shifted Soil Fungal but Not Bacterial Community Composition.

Copper-based fungicides are routinely used for wood and plant protection, which can lead to an enrichment of copper-tolerant microbial communities in soil. To investigate the effect of such wood preservatives on the soil fungal and bacterial community compositions, five different vineyard and fruit-growing soil environments were evaluated using incubation studies over time. Pine sapwood specimens were impregnated with either water or different biocide treatment solutions containing a mixture of copper, triazoles, and quaternary ammonium compounds (CuTriQAC), a mixture of triazoles and quaternary ammonium compounds (TriQAC), or copper alone (Cu). Specimens were incubated in soil from each sample site for 8, 16, 24, and 32 weeks. The effects of preservative treatment on the modulus of elasticity (MOE) of the wood specimens and on the soil fungal as well as bacterial community composition at the soil-wood interface were assessed by quantitative PCR and amplicon sequencing of the fungal internal transcribed spacer (ITS) region and bacterial 16S rRNA gene. Specimens impregnated with CuTriQAC and Cu showed decreased MOE and reduced fungal and bacterial copy numbers over time compared to those impregnated with water and TriQAC. Fungal but not bacterial community composition was significantly affected by wood preservative treatment. The relative abundance of members of the family Trichocomaceae compared to other genera increased in the presence of the Cu and CuTriQAC treatments at three sites, suggesting these to be Cu-tolerant fungi. In conclusion, the copper-containing treatments resulted in marginally increased MOE, lowered microbial gene copy numbers compared to those in the TriQAC and water treatments, and thus enhanced wood protection against soil microbial wood degradation.IMPORTANCE Copper-containing rather than TRIQAC formulations are efficient wood preservatives irrespective of the origin and composition of the soil microbial communities. However, some fungi appear to be naturally insensitive to copper and should be the focus of future wood preservative formulations to facilitate the life span of wooden construction in contact with soil while also minimizing the overall environmental impact.

Temperature impacts differentially on the methanogenic food web of cellulose-supplemented peatland soil.

The impact of temperature on the largely unresolved intermediary ecosystem metabolism and associated unknown microbiota that link cellulose degradation and methane production in soils of a moderately acidic (pH 4.5) fen was investigated. Supplemental [(13) C]cellulose stimulated the accumulation of propionate, acetate and carbon dioxide as well as initial methane production in anoxic peat soil slurries at 15°C and 5°C. Accumulation of organic acids at 15°C was twice as fast as that at 5°C. 16S rRNA [(13) C]cellulose stable isotope probing identified novel unclassified Bacteria (79% identity to the next cultured relative Fibrobacter succinogenes), unclassified Bacteroidetes (89% identity to Prolixibacter bellariivorans), Porphyromonadaceae, Acidobacteriaceae and Ruminococcaceae as main anaerobic degraders of cellulose-derived carbon at both 15°C and 5°C. Holophagaceae and Spirochaetaceae were more abundant at 15°C. Clostridiaceae dominated the degradation of cellulose-derived carbon only at 5°C. Methanosarcina was the dominant methanogenic taxa at both 15°C and 5°C. Relative abundance of Methanocella increased at 15°C whereas that of Methanoregula and Methanosaeta increased at 5°C. Thaumarchaeota closely related to Nitrosotalea (presently not known to grow anaerobically) were abundant at 5°C but absent at 15°C indicating that Nitrosotalea sp. might be capable of anaerobic growth at low temperatures in peat.

Significant nonsymbiotic nitrogen fixation in Patagonian ombrotrophic bogs.

Nitrogen (N) nutrition in pristine peatlands relies on the natural input of inorganic N through atmospheric deposition or biological dinitrogen (N2 ) fixation. However, N2 fixation and its significance for N cycling, plant productivity, and peat buildup are mostly associated with the presence of Sphagnum mosses. Here, we report high nonsymbiotic N2 -fixation rates in two pristine Patagonian bogs with diversified vegetation and natural N deposition. Nonsymbiotic N2 fixation was measured in samples from 0 to 10, 10 to 20, and 40 to 50 cm depth using the (15) N2 assay as well as the acetylene reduction assay (ARA). The ARA considerably underestimated N2 fixation and can thus not be recommended for peatland studies. Based on the (15) N2 assay, high nonsymbiotic N2 -fixation rates of 0.3-1.4 µmol N2  g(-1)  day(-1) were found down to 50 cm under micro-oxic conditions (2 vol.%) in samples from plots covered by Sphagnum magellanicum or by vascular cushion plants, latter characterized by dense and deep aerenchyma roots. Peat N concentrations point to greater potential of nonsymbiotic N2 fixation under cushion plants, likely because of the availability of easily decomposable organic compounds and oxic conditions in the rhizosphere. In the Sphagnum plots, high N2 fixation below 10 cm depth rather reflects the potential during dry periods or low water level when oxygen penetrates the top peat layer and triggers peat mineralization. Natural abundance of the (15) N isotope of live Sphagnum (5.6 δ‰) from 0 to 10 cm points to solely N uptake from atmospheric deposition and nonsymbiotic N2 fixation. A mean (15) N signature of -0.7 δ‰ of peat from the cushion plant plots indicates additional N supply from N mineralization. Our findings suggest that nonsymbiotic N2 fixation overcomes N deficiency in different vegetation communities and has great significance for N cycling and peat accumulation in pristine peatlands.

Agricultural soil and drilosphere as reservoirs of new and unusual assimilators of 2,4-dichlorophenol carbon.

2,4-Dichlorophenol (2,4-DCP) is a potential soil and groundwater contaminant. Earthworms modulate growth and activities of soil microbiota. Thus, active 2,4-DCP degraders in agricultural soil and drilosphere (i.e. burrow walls, gut content and cast) were identified by comparative amplicon pyrosequencing-based 16S rRNA stable isotope probing in soil columns. In situ relevant concentrations of [U-(13) C]2,4-DCP were consumed in soil within 19 and 41 days in the presence and absence of the endogeic earthworm Aporrectodea caliginosa, respectively. [U-(14) C]2,4-DCP mineralization was higher in cast, burrow wall and soil from columns with than without earthworms. [U-(14) C]2,4-DCP mineralization was lowest in gut contents. Data indicated a strong impact of earthworms on the active microbial community. Novosphingobium, Comamonas and Desulfitobacterium sp. assimilated 2,4-DCP-[(13)C] in the absence of earthworms. Pseudomonas, Flavobacterium and Clostridium sp. assimilated 2,4-DCP-[(13)C] in the drilosphere. Novosphingobium- and Variovorax-related taxa dominated [U-(13)C]2,4-DCP consumers in soil slurries with drilosphere and bulk soil material. 16S rRNA sequences suggested species level novelty. The collective data demonstrates that new Bacteroidetes and Alphaproteobacteria/Betaproteobacteria were involved in 2,4-DCP-C transformation and indicated that diverse and hitherto unknown microbes associated with carbon flow from 2,4-DCP are shaped by earthworms.

Specialized biopolymers: versatile tools for microbial resilience.

Bacteria produce a wide range of specialized biopolymers that can be classified into polysaccharides, polyamides, and polyesters and are considered to fulfill storage functions. In this review, we highlight recent developments in the field linking metabolism of biopolymers to stress and signaling physiology of the producers and demonstrating that biopolymers contribute to bacterial stress resistance and shape structure and composition of microenvironments. While specialized biopolymers are currently the focus of much attention in biotechnology as innovative and biodegradable materials, our understanding about the regulation and functions of these valuable compounds for the producers, microbial communities, and our environment is still very limited. Addressing open questions about signals, mechanisms, and functions in the area of biopolymers harbors potential for exciting discoveries with high relevance for biotechnology and fundamental research.

Setting new standards: Multiphasic analysis of microplastic mineralization by fungi.

Plastic materials provide numerous benefits. However, properties such as durability and resistance to degradation that make plastic attractive for variable applications likewise foster accumulation in the environment. Fragmentation of plastics leads to the formation of potentially hazardous microplastic, of which a considerable amount derives from polystyrene. Here, we investigated the biodegradation of polystyrene by the tropical sooty mold fungus Capnodium coffeae in different experimental setups. Growth of C. coffeae was stimulated significantly when cultured in presence of plastic polymers rather than in its absence. Stable isotope tracing using 13C-enriched polystyrene particles combined with cavity ring-down spectroscopy showed that the fungus mineralized polystyrene traces. However, phospholipid fatty acid stable isotope probing indicated only marginal assimilation of polystyrene-13C by C. coffeae in liquid cultures. NMR spectroscopic analysis of residual styrene contents prior to and after incubation revealed negligible changes in concentration. Thus, this study suggests a plastiphilic life style of C. coffeae despite minor usage of plastic as a carbon source and the general capability of sooty mold fungi to stimulate polystyrene mineralization, and proposes new standards to identify and unambiguously demonstrate plastic degrading capabilities of microbes.

Resilience of aerobic methanotrophs in soils; spotlight on the methane sink under agriculture.

Aerobic methanotrophs are a specialized microbial group, catalyzing the oxidation of methane. Disturbance-induced loss of methanotroph diversity/abundance, thus results in the loss of this biological methane sink. Here, we synthesized and conceptualized the resilience of the methanotrophs to sporadic, recurring, and compounded disturbances in soils. The methanotrophs showed remarkable resilience to sporadic disturbances, recovering in activity and population size. However, activity was severely compromised when disturbance persisted or reoccurred at increasing frequency, and was significantly impaired following change in land use. Next, we consolidated the impact of agricultural practices after land conversion on the soil methane sink. The effects of key interventions (tillage, organic matter input, and cover cropping) where much knowledge has been gathered were considered. Pairwise comparisons of these interventions to nontreated agricultural soils indicate that the agriculture-induced impact on the methane sink depends on the cropping system, which can be associated to the physiology of the methanotrophs. The impact of agriculture is more evident in upland soils, where the methanotrophs play a more prominent role than the methanogens in modulating overall methane flux. Although resilient to sporadic disturbances, the methanotrophs are vulnerable to compounded disturbances induced by anthropogenic activities, significantly affecting the methane sink function.

Mitomycin C-induced effects on aerobic methanotrophs in a landfill cover soil; implications of a viral shunt?

A viral shunt can occur when phages going through a lytic cycle, including lysogenic phages triggered by inducing agents (e.g. mitomycin C), results in host lysis and the release of cell constituents and virions. The impact of a viral shunt on the carbon, including methane cycle in soil systems is poorly understood. Here, we determined the effects of mitomycin C on the aerobic methanotrophs in a landfill cover soil. To an extent, our results support a mitomycin C-induced viral shunt, as indicated by the significantly higher viral-like particle (VLP) counts relative to bacteria, elevated nutrient concentrations (ammonium, succinate), and initially impaired microbial activities (methane uptake and microbial respiration) after mitomycin C addition. The trend in microbial activities at <2 days largely corresponded to the expression of the pmoA and 16S rRNA genes. Thereafter (>11 days), the active bacterial community composition significantly diverged in the mitomycin C-supplemented incubations, suggesting the differential impact of mitomycin C on the bacterial community. Collectively, we provide insight on the effects of mitomycin C, and potentially a viral shunt, on the bacteria in the soil environment.

Interkingdom interaction: the soil isopod Porcellio scaber stimulates the methane-driven bacterial and fungal interaction.

Porcellio scaber (woodlice) are (sub-)surface-dwelling isopods, widely recognized as "soil bioengineers", modifying the edaphic properties of their habitat, and affecting carbon and nitrogen mineralization that leads to greenhouse gas emissions. Yet, the impact of soil isopods on methane-cycling processes remains unknown. Using P. scaber as a model macroinvertebrate in a microcosm study, we determined how the isopod influences methane uptake and the associated interaction network in an agricultural soil. Stable isotope probing (SIP) with 13C-methane was combined to a co-occurrence network analysis to directly link activity to the methane-oxidizing community (bacteria and fungus) involved in the trophic interaction. Compared to microcosms without the isopod, P. scaber significantly induced methane uptake, associated to a more complex bacteria-bacteria and bacteria-fungi interaction, and modified the soil nutritional status. Interestingly, 13C was transferred via the methanotrophs into the fungi, concomitant to significantly higher fungal abundance in the P. scaber-impacted soil, indicating that the fungal community utilized methane-derived substrates in the food web along with bacteria. Taken together, results showed the relevance of P. scaber in modulating methanotrophic activity with implications for bacteria-fungus interaction.