In situ metabolic activities of uncultivated Ferrovum sp. CARN8 evidenced by metatranscriptomic analysis

Towards an understanding of the factors controlling bacterial diversity and activity in semi-passive Fe- and As-oxidizing bioreactors treating arsenic-rich acid mine drainage

Semi-passive bioreactors based on iron and arsenic oxidation and coprecipitation are promising for the treatment of As-rich acid mine drainages. However, their performance in the field remains variable and unpredictable. Two bioreactors filled with distinct biomass carriers (plastic or a mix of wood and pozzolana) were monitored during 1 year. We characterized the dynamic of the bacterial communities in these bioreactors, and explored the influence of environmental and operational drivers on their diversity and activity. Bacterial diversity was analyzed by 16S rRNA gene metabarcoding. The aioA genes and transcripts were quantified by qPCR and RT-qPCR. Bacterial communities were dominated by several iron-oxidizing genera. Shifts in the communities were attributed to operational and physiochemical parameters including the nature of the biomass carrier, the water pH, temperature, arsenic, and iron concentrations. The bioreactor filled with wood and pozzolana showed a better resilience to disturbances, related to a higher bacterial alpha diversity. We evidenced for the first time aioA expression in a treatment system, associated with the presence of active Thiomonas spp. This confirmed the contribution of biological arsenite oxidation to arsenic removal. The resilience and the functional redundancy of the communities developed in the bioreactors conferred robustness and stability to the treatment systems.

Post-measurement compressed calibration for ICP-MS-based metal quantification in mine residues bioleaching

Bioleaching is an actual economical alternative to treat residues, which allows, depending on the chosen strategy, two possible outcomes: (1) a leachate enriched with target metals, or (2) a residue enriched in target metals through the leaching of interfering components (IC). This work aimed to study the metals released by bioprocessing the Panasqueira mine tailings, as a strategy to increase critical metals' relative concentration in residues. Biostimulation of the local microbiota was compared to a bioaugmentation approach using the autochthonous Diaphorobacter polyhydroxybutyrativorans strain B2A2W2. Inductively Coupled Plasma Mass Spectrometry (ICP-MS) was selected to study the metals released in the leachate through multi-element external standards. A new data treatment method was developed to use a preliminary sweep of intensities to quantify the non-initial target metals concentration in the leachate, based on preliminary ICP-MS intensity measurements. The results demonstrated that biostimulation was an efficient bioleaching strategy for the IC silicon, aluminium, magnesium, selenium, manganese, zinc, iron, and copper, by decreasing concentration, resulting in a relative increase in the gallium and yttrium (10x) levels in the treated residue. The strategy followed to quantify a large number of elements with ICP-MS using a reduced number of data points for calibration proved valid and speeded up the analytical process.

Advancement of Metatranscriptomics towards Productive Agriculture and Sustainable Environment: A Review

While chemical fertilisers and pesticides indeed enhance agricultural productivity, their excessive usage has been detrimental to environmental health. In addressing this matter, the use of environmental microbiomes has been greatly favoured as a ‘greener’ alternative to these inorganic chemicals’ application. Challenged by a significant proportion of unidentified microbiomes with unknown ecological functions, advanced high throughput metatranscriptomics is prudent to overcome the technological limitations in unfolding the previously undiscovered functional profiles of the beneficial microbiomes. Under this context, this review begins by summarising (1) the evolution of next-generation sequencing and metatranscriptomics in leveraging the microbiome transcriptome profiles through whole gene expression profiling. Next, the current environmental metatranscriptomics studies are reviewed, with the discussion centred on (2) the emerging application of the beneficial microbiomes in developing fertile soils and (3) the development of disease-suppressive soils as greener alternatives against biotic stress. As sustainable agriculture focuses not only on crop productivity but also long-term environmental sustainability, the second half of the review highlights the metatranscriptomics’ contribution in (4) revolutionising the pollution monitoring systems via specific bioindicators. Overall, growing knowledge on the complex microbiome functional profiles is imperative to unlock the unlimited potential of agricultural microbiome-based practices, which we believe hold the key to productive agriculture and sustainable environment.

Population Genomics of Microbial Biostalactites: Non-recombinogenic Genome Islands and Microdiversification by Transposons

Intrapopulation genetic variability in prokaryotes is receiving increasing attention thanks to improving sequencing methods; however, the ability to distinguish intrapopulation variability from species clusters or initial stages of gene flow barrier development remains insufficient. To overcome this limitation, we took advantage of the lifestyle of Ferrovum myxofaciens, a species that may represent 99% of prokaryotic microbiome of biostalactites growing at acid mine drainage springs. We gained four complete and one draft metagenome-assembled F. myxofaciens genomes using Oxford Nanopore and Illumina sequencing and mapped the reads from each sample on the reference genomes to assess the intrapopulation variability. We observed two phenomena associated with intrapopulation variability: hypervariable regions affected by mobilome expansion called “scrapyards,” and variability in gene disruptions caused by transposons within each population. Both phenomena were previously described in prokaryotes. However, we present here for the first time scrapyard regression and the development of a new one. Nearly complete loss of intrapopulation short sequence variability in the old scrapyard and high variability in the new one suggest that localized gene flow suppression is necessary for scrapyard formation. Concerning the variable gene disruptions, up to 9 out of 41 occurrences per sample were located in highly conserved diguanylate cyclases/phosphodiesterases. We propose that microdiversification of life strategies may be an adaptive outcome of random diguanylate cyclase elimination. The mine biostalactites thus proved as a unique model system for describing genomic intrapopulation processes, as they offer easily sampleable units enriched in a single microbial species.

Water and soil contaminated by arsenic: the use of microorganisms and plants in bioremediation

Owing to their roles in the arsenic (As) biogeochemical cycle, microorganisms and plants offer significant potential for developing innovative biotechnological applications able to remediate As pollutions. This possible use in bioremediation processes and phytomanagement is based on their ability to catalyse various biotransformation reactions leading to, e.g. the precipitation, dissolution, and sequestration of As, stabilisation in the root zone and shoot As removal. On the one hand, genomic studies of microorganisms and their communities are useful in understanding their metabolic activities and their interaction with As. On the other hand, our knowledge of molecular mechanisms and fate of As in plants has been improved by laboratory and field experiments. Such studies pave new avenues for developing environmentally friendly bioprocessing options targeting As, which worldwide represents a major risk to many ecosystems and human health.