In temperate European forests, soil fungal communities, dominated by saprotrophic and ectomycorrhizal (ECM) species, represent almost 25% of soil organic carbon (C) in the soil. However, the decomposition dynamics of fungal necromass, the bioavailability of its associated elements and its role in soil C stabilisation remain poorly understood. We investigated how intrinsic chemical properties-particularly melanin content, nitrogen (N) and phosphorus (P) levels-influence the microbial decomposition of fungal necromass in a temperate oak forest. We compared two types of fungal necromass: Laccaria bicolor (low melanin content) and Fomitiporia robusta (high melanin content). We monitored mass loss, stoichiometric ratios and microbial enzymatic activity over a six-month period in soil. Additionally, we analysed bacterial and fungal community structures via DNA metabarcoding, and estimated microbial biomass using qPCR during the decomposition process. The highly melanised necromass showed limited mass loss and reduced enzymatic activity, indicating greater recalcitrance. Contrasting C:P and C:N ratio profiles during the decomposition of the two types of substrate suggest that melanin plays a key role in the decomposition dynamics of the fungal necromass, while P and N do not appear to be determining factors in this process. Copiotrophic bacteria and saprotrophic fungi dominated the early stages of decomposition, while in later stages, oligotrophic bacteria and certain ECM genera became dominant. Our findings confirm that fungal necromass decomposition is strongly influenced by its intrinsic chemical properties, and particularly by its melanin content. This substrate constitutes a unique ecological niche, shaping the succession of specialised microbial guilds (i.e. the fungal necrobiome). Finally, our results highlight the significant abundance of certain fungal guilds, such as ECM fungi, raising questions about the potential role of these symbiotic fungi in the decomposition of fungal necromass or their passive, but massive, colonisation of this soil micro-niche.Read the free for this article on the Journal blog.

Polyhydroxyalkanoates (PHAs) are promising biobased and biodegradable alternatives to conventional plastics, yet their degradation mechanisms and the diversity of microorganisms involved remain poorly characterized in marine ecosystems. Here, we used 13C-labeled poly(3-hydroxybutyrate) (PHB) and combined DNA-stable isotope probing (DNA-SIP) with metagenomic to identify and functionally characterize active PHB-degrading bacteria in seawater. We identified three metagenome-assembled genomes (MAGs) affiliated with the genus Agarilytica that exhibited an exceptional expansion of preficted extracellular short-chain-length PHA depolymerase genes (ephaZscl) with up to 14 copies per genome, far exceeding the one-to-two copies typically reported. Comparative genomic and structural analyses revealed gene duplication and fusion events, given rise to tandem or chimeric depolymerases that may enhance catalytic diversity and substrate accessibility. Three-dimensional structural modeling confirmed that these fusion proteins retained functional catalytic domains with potential cooperative or independent activity. Such genomic redundancy and structural diversification likely confer an adaptive advantage for PHB biodegradation in marine environment. Collectively, our findings provide new insights into the ecological and evolutionary strategies of marine PHB degraders and highlight the power of DNA-SIP metagenomic for elucidating active plastic biodegradation pathways under natural conditions.

There is still a need for a better understanding of how abiotic/biotic factors affect the functional structure and composition of biological assemblages, given that living organisms are in constant interaction with their environment and with each other. Here, we present a comprehensive dataset of 31 functional traits of bacteria using information from BacDive, a bacterial diversity meta-database, as well as from the rrnDB and genomesizeR datasets. This updated version of the BactoTraits dataset, in addition to now offering more traits for more strains (97,721 strains with at least one trait described), makes R scripts available to the scientific community. These traits include physiological characteristics, metabolic processes, genome properties and biotope preferences. They could be inferred to the whole bacterial community thanks to taxonomic affiliation obtained from traditional high throughput 16S rRNA gene amplicon sequencing methods. This taxonomic affiliation is based on the regularly updated SILVA database and thus allows to study combinations of weighted mean trait profiles of bacterial communities at different taxonomic levels. BactoTraits can be used, for example, to improve predictions of ecological responses to natural/anthropogenic pressures and to support biomonitoring, management and conservation strategies. The R scripts, as well as the dataset encoded in BactoTraits, are available at: https://doi.org/10.24396/ORDAR-182.

ABSTRACT Northern regions of France have historically experienced mining and steel production activities, leading to the emergence of multi‐contaminated soils by metals. These metals are a source of indirect disruption to ecosystem functioning through the alteration of biodiversity. We focused on spiders, which are major regulators of terrestrial ecosystems, acting simultaneously as prey, predators and competitors in soil communities. The aim of this study was to assess the impact of metal contamination, among a set of environmental parameters, on the taxonomic and functional structures of spider communities; to identify indicator spider species; and to define trait syndromes specific to metal‐contaminated wastelands. We sampled spiders in 40 sites that represented a metal‐contamination gradient. We have shown that certain environmental parameters largely account for the taxonomic and functional structure of spider assemblages (e.g., soil granulometry, vegetation, pH). The concentrations of metals in the soil (Ag, Al, As, Cd, Mn, Pb, Sb and Zn) also had a significant but less pronounced impact. We have identified Xerolycosa nemoralis (Lycosidae) as an interesting indicator of metal‐contaminated environments. Furthermore, the contaminated sites contained fewer indicator species than the reference areas. Forested and herbaceous landscape promoted the presence of sheet‐ and orb‐web weavers, respectively. Although metal contamination was not the only driver of this trend, stenophagous spiders, which prefer to retreat and hunt on the ground, were selected at most contaminated sites surrounded by sealed ground, which corresponded to a selection of A‐strategists. The observed trends could be explained by the age of the contamination, the low bioavailability of the metals, the spiders' dispersal capacity, or their effective adaptative mechanisms that mitigate the direct impact of soil contamination on spider assemblages. A better understanding of the role of metals in shaping biological communities can provide valuable insights, particularly regarding ecosystem functioning, environmental monitoring and restoration of contaminated areas.

Polycyclic aromatic hydrocarbon (PAH) contamination in industrial soils poses significant environmental challenges, necessitating cost-effective bioremediation approaches like tree-based phytoremediation. However, the defence mechanisms and adaptability of trees to PAH exposure remain poorly understood, while the identification of molecular markers could help in the detection of toxicity symptoms. This study explores the molecular response of Populus canadensis to a phenanthrene (PHE) contamination gradient (from 100 to 2000 mg kg−1) using RNA-seq analysis of roots and leaves after 4 weeks of exposure. Both differentially expressed genes (DEGs) and DRomics, a dose–response tool, identified transcriptomic changes, with about 50

Dinitrogen (N₂) fixation by diazotrophs supports ocean productivity. Diazotrophs include photoautotrophic cyanobacteria, non-cyanobacterial diazotrophs (NCDs), and the recently discovered N2-fixing haptophyte. While NCDs are ubiquitous in the ocean, their ecology and metabolism remain largely unknown. Unlike cyanobacterial diazotrophs and the haptophyte, NCDs are primarily heterotrophic and depend on dissolved organic matter (DOM) for carbon and energy. However, conventional DOM amendment incubations do not allow discerning how different diazotrophs use DOM molecules, limiting our knowledge on DOM-diazotroph interactions. To identify diazotrophs using DOM, we amended North Pacific microbial communities with 13C-labeled DOM from phytoplankton cultures that was molecularly characterized, revealing the dominance of nitrogen-rich compounds. After DOM additions, we observed a community shift from cyanobacterial diazotrophs like Crocosphaera and Trichodesmium to NCDs at stations where the N2-fixing haptophyte abundance was relatively low. Through DNA stable isotope probing and gene sequencing, we identified diverse diazotrophs capable of taking up DOM. Our findings highlight unexpected DOM uptake by the haptophyte's nitroplast, changes in community structure, and previously unrecognized osmotrophic behavior in NCDs, shaped by local biogeochemical conditions.

Phytoremediation using trees has become popular due to its effectiveness and affordability, including for brownfield soils contaminated with polycyclic aromatic hydrocarbons (PAH). However, our understanding of how trees cope with exposure to PAHs is limited. In this study, we employed an innovative experimental design combining a contamination gradient of eight phenanthrene concentrations (0-2000 mg·kg⁻¹), a model PAH, with a comprehensive integrative multi-omics approach (transcriptomics, proteomics, and metabolomics) to study the physiological responses of poplar (Populus x canadensis). The objective was to identify molecular biomarkers from poplar roots and leaves. This pioneering setup generated large datasets: 27,561 transcripts, 6787 proteins, and 2799 metabolites for roots, and 26,079 transcripts, 8249 proteins, and 2239 metabolites for leaves. The datasets were integrated using the mixOmics package, highlighting a distinct response between the lowest and highest phenanthrene concentrations for roots and the combinaison of roots and leaves (tipping point at 400 mg.kg-1), and between PHE-spiked and unspiked control for leaves. Different metabolic pathways were identified as plant biomarkers at low and high PHE concentrations. These biomarkers were specific for low and high toxicity, respectively. The most affected pathways were carbon fixation, oxidative phosphorylation, glycerolipid metabolism at low PHE concentrations, starch and sucrose metabolism, and aminoacyl-tRNA biosynthesis at high PHE concentrations. In total, 73 relevant biomarkers were identified from photosynthesis to flavonoid biosynthesis pathways. These results highlight the key molecular mechanisms triggered by poplar in response to PAH contamination and suggest molecular targets of interest for future ecotoxicity tests.

The microbial biodegradation potential of contaminated sites is critical for efficient bioremediation, particularly through bioaugmentation with microorganisms that degrade organic pollutants. The BactoTrapS tool was developed to select and enrich bacteria tolerant to contaminants and capable of biodegradation directly from soils. It comprises a nylon mesh filled with activated carbon or vermiculite spiked with PAHs (phenanthrene, pyrene, dibenzo-a,h-anthracene) or alkanes (n-hexadecane, cyclohexane), while control traps remained unspiked. After five weeks of soil incubation, spiked traps showed significantly higher mineralisation. Bacterial colonisation was evaluated via CFU counts and 16S rDNA qPCR, revealing increased densities in spiked conditions. Alpha diversity analysis showed reduced diversity in spiked traps, while beta diversity confirmed selective enrichment of genera such as Mycobacterium and Polaromonas under PAHs, and Nocardioides and Nocardia under alkanes. These genera were identified as indicator species for the respective contaminants. qPCR of key biodegradation genes (PAH-RHDα, AlkB, CYP153) revealed elevated gene copy numbers in spiked traps. Most isolates from spiked conditions metabolised phenanthrene and hexadecane as sole carbon sources. BactoTrapS offers a rapid, efficient method to enrich biodegrading bacteria for hydrocarbons and other organic contaminants, promising broad applicability for future remediation efforts.

Although involved in key functions of the terrestrial ecosystems, the activity and the diversity of soil microorganisms can be severely limited by energy and nutrients in weathered tropical soils. To optimize nutrient cycling for crop nutrition, assessing which nutrients limit the activity of the microbial food web is thus essential. This was our aim in this study carried out on a tropical ferrallitic soil from a natural grassland in Madagascar. For this purpose, we employed an innovative nutrient-omission approach in microcosms to test the distinct effects of omitting C, six nutrients (N, P, K, S, Ca, Mg) and a cocktail of micronutrients (B, Mn, Cu, Na and Mo) on the composition, biomass and activities of the microbial community and on the abundance and biomass of their nematode grazers. C and P were identified as primary limitations, but other nutrients (N, Mg and S) played significant roles as co-limiting factors. Some bacterial and fungal taxa were significantly associated to specific nutrient deficiencies and can act as biological indicators. Additionally, the abundance and biomass of microbial-feeding nematodes provided valuable insights into the responses of the soil microbial community to nutrient deficiencies. These findings contribute to our understanding of nutrient dynamics and microbial community growth in tropical grassland ecosystems and have implications for sustainable crop fertility management and ecosystem ecology in similar environments.

Polychlorinated biphenyls (PCBs) are recognized as persistent organic pollutants and accumulate in organisms, soils, waters, and sediments, causing major health and ecological perturbations. Literature reported PCB bio-transformation by fungi and bacteria in vitro, but data about the in situ impact of those compounds on microbial communities remained scarce while being useful to guide biotransformation assays. The present work investigated for the first time microbial diversity from the three-domains-of-life in a long-term contaminated brownfield (a former factory land). Soil samples were ranked according to their PCB concentrations, and a significant increase in abundance was shown according to increased concentrations. Microbial communities structure showed a segregation from the least to the most PCB-polluted samples. Among the identified microorganisms, Bacteria belonging to Gammaproteobacteria class, as well as Fungi affiliated to Saccharomycetes class or Pleurotaceae family, including some species known to transform some PCBs were abundantly retrieved in the highly polluted soil samples.

The land-sea continuum constitutes a mixing zone where soil microbial communities encounter, via runoff, those inhabiting marine coastal sediment resulting in community coalescence. Here, we propose an experimental approach, mimicking the land-sea continuum, to study the microbial community coalescence events in different situations, by 16S and 18S rRNA genes metabarcoding. The microbial community structure of sediment diverged with the soil inputs. For prokaryotes, phylogenetic enrichment and amplicon sequence variants (ASVs) replacements characterized the community changes in sediment receiving soil inputs. For fungi, despite phylogenetic enrichment was not observed, the fungal ASVs richness was maintained by soil inputs. Comparison of microbial communities revealed ASVs specific to sediment receiving soil inputs, and also ASVs shared with soil and/or runoff. Among these specific ASVs, four bacterial and one fungal ASVs were identified as indicators of coalescence. Our study provides evidences that coalescence involves the mixing of microorganisms and of the environment.

Abstract Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds. Thus, they are crucial for the development of nature-based solutions to reduce pollution and of bio-based solutions for environmental risk assessment of chemicals. At the intersection between microbial ecology, toxicology, and biogeochemistry, microbial ecotoxicology is a fast-expanding research area aiming to decipher the interactions between pollutants and microorganisms. This perspective paper gives an overview of the main research challenges identified by the Ecotoxicomic network within the emerging One Health framework and in the light of ongoing interest in biological approaches to environmental remediation and of the current state of the art in microbial ecology. We highlight prevailing knowledge gaps and pitfalls in exploring complex interactions among microorganisms and their environment in the context of chemical pollution and pinpoint areas of research where future efforts are needed.

A contamination gradient of phenanthrene affected the soil bacterial community at both taxonomic and functional levels but the poplar root bacterial endophytome was not modified. Polycyclic aromatic hydrocarbon (PAH) contamination of industrial wasteland soils affects microbial diversity, but little is known about the dose-response effects of such contaminants on taxonomic and functional diversities of rhizospheric and plant endophytic bacteria. This study focused on the response of soil and root bacterial communities associated to poplar grown in a contamination gradient of phenanthrene (PHE). It was hypothesized that the increase in contamination would modify gradually the bacterial diversity and functions. The effects of the PHE contamination were limited to soil communities and did not affect the poplar root endophytome where Streptomyces and Cutibacterium were the most abundant genera. Along the PHE gradient, alpha-diversity indices decreased and the community structure of soil bacteria at the taxonomic level shifted. The abundance of genes involved in PAH-degradation pathways and the relative proportion of certain microbial taxa such as Polaromonas, Sphingopyxis, Peredibacter, Phenylobacterium, Ramlibacter, Sphingomonas, and Pseudomonas, often described as potential PAH biodegraders, increased with the PHE concentration in the soil community. Conversely, the contamination negatively impacted other taxa like Nocardioides, Streptomyces, Gaiella, Solirubrobacter, Bradyrhizobium, and Nitrospira. Functional inference and enzymatic activity measurements revealed that some bacterial functions related to carbon, nitrogen and phosphorus cycles were modified in soil throughout the PHE gradient. This study allowed a deeper understanding of the complex plant-bacteria interactions in the case of soil PAH contamination and the potential impact on soil functioning.

An experimental approach mimicking the land-sea continuum in microcosms was developed in order to determine the effect of the terrigenous inputs by soil runoff on the microbial functional potential in hydrocarbon (HC) contaminated marine coastal sediment. We hypothesized that the coalescent event increases the functional potential of microbial communities in marine coastal sediments, influencing the fate of HC in marine coastal ecosystems. The microbial functional potential including the HC degradation ability was assessed by DNA-array to compare the sediment receiving or not terrigenous inputs. The removal of HC and the functional gene richness in sediment was unchanged with the terrigenous inputs. However, the gene variants (GVs) composition was modified indicating functional redundancy. In addition, functional indicators including GVs related to sulfite reduction, denitrification and polyaromatic degradation were identified in higher proportion in sediment receiving terrigenous inputs. The terrigenous inputs modified the functional co-occurrence networks, showing a reorganization of the GVs associations with an increase of the network complexity. Different keystone GVs ensuring similar functions were identified in networks with or without terrigenous inputs, further confirming functional redundancy. We argue that functional redundancy maintains the structure of microbial community in hydrocarbon-contaminated land-sea continuum mixing zone. Our results provide helpful functional information for the monitoring and management of coastal environment affected by human land-based activities.

EDITORIAL article Front. Microbiol., 23 March 2022Sec. Microbiotechnology https://doi.org/10.3389/fmicb.2022.870404

All living organisms theoretically have an optimal stoichiometric nitrogen: phosphorus (N: P) ratio, below and beyond which their growth is affected, but data remain scarce for microbial decomposers. Here, we evaluated optimal N: P ratios of microbial communities involved in cellulose decomposition and assessed their stability when exposed to copper Cu(II). We hypothesized that (1) cellulose decomposition is maximized for an optimal N: P ratio; (2) copper exposure reduces cellulose decomposition and (3) increases microbial optimal N: P ratio; and (4) N: P ratio and copper modify the structure of microbial decomposer communities. We measured cellulose disc decomposition by a natural inoculum in microcosms exposed to a gradient of N: P ratios at three copper concentrations (0, 1 and 15 mu M). Bacteria were most probably the main decomposers. Without copper, cellulose decomposition was maximized at an N: P molar ratio of 4.7. Contrary to expectations, at high copper concentration, the optimal N: P ratio (2.8) and the range of N: P ratios allowing decomposition were significantly reduced and accompanied by a reduction of bacterial diversity. Copper contamination led to the development of tolerant taxa probably less efficient in decomposing cellulose. Our results shed new light on the understanding of multiple stressor effects on microbial decomposition in an increasingly stoichiometrically imbalanced world. Copper contamination reduces the optimal N: P ratio and the range of N: P ratios for cellulose decomposition by bacterial decomposers.