Technical advances have converted bioremediation into a large-scale ecosystem service suitable for the treatment of polluted soils worldwide; however, its application in Chile is scarce. The main hurdles that must be addressed include the capacities of such approaches for the treatment of polluted soils, the lack of knowledge about key factors affecting bioremediation costs and the lack of a legal framework to regulate this activity. In this study, the economic performance of the bioremediation of chronically hydrocarbon-polluted urban soils based on bioaugmentation, biostimulation or the combination of both approaches projected to an industrial scale was evaluated. The cost of bioremediation ranged between USD 50.7 and USD 310.4 per m³ of contaminated soil. In addition, the items and activities that had the most significant impacts on the final bioremediation cost, such as compost for biostimulation and bacterial growth media for bioaugmentation-based approaches, were identified. The projected costs were compared against an extensive database of 130 soil bioremediation projects. The bioremediation treatment costs fell within the top 60% of the more expensive projects, highlighting the high effort involved in bioremediation of chronically contaminated soils. This framework can facilitate the decision making of entrepreneurs, consultants, researchers and governmental authorities when launching initiatives to develop a local bioremediation industry capable of cleaning up a high number of polluted sites in Chile.

The production of lignocellulosic-derived biofuels is a highly promising source of alternative energy, but it has been constrained by the lack of a microbial platform capable to efficiently degrade this recalcitrant material and cope with by-products that can be toxic to cells. Species that naturally grow in environments where carbon is mainly available as lignin are promising for finding new ways of removing the lignin that protects cellulose for improved conversion of lignin to fuel precursors. Enterobacter lignolyticus SCF1 is a facultative anaerobic Gammaproteobacteria isolated from tropical rain forest soil collected in El Yunque forest, Puerto Rico under anoxic growth conditions with lignin as sole carbon source. Whole transcriptome analysis of SCF1 during E.lignolyticus SCF1 lignin degradation was conducted on cells grown in the presence (0.1%, w/w) and the absence of lignin, where samples were taken at three different times during growth, beginning of exponential phase, mid-exponential phase and beginning of stationary phase. Lignin-amended cultures achieved twice the cell biomass as unamended cultures over three days, and in this time degraded 60% of lignin. Transcripts in early exponential phase reflected this accelerated growth. A complement of laccases, aryl-alcohol dehydrogenases, and peroxidases were most up-regulated in lignin amended conditions in mid-exponential and early stationary phases compared to unamended growth. The association of hydrogen production by way of the formate hydrogenlyase complex with lignin degradation suggests a possible value added to lignin degradation in the future.

Some sulfate-reducing bacteria (SRB), mainly belonging to the Desulfovibrionaceae family, have evolved the capability to conserve energy through microbial extracellular electron transfer (EET), suggesting that this process may be more widespread than previously believed. While previous evidence has shown that mobile genetic elements drive the plasticity and evolution of SRB and iron-reducing bacteria (FeRB), few have investigated the shared molecular mechanisms related to EET. To address this, we analyzed the prevalence and abundance of EET elements and how they contributed to their differentiation among 42 members of the Desulfovibrionaceae family and 23 and 59 members of Geobacteraceae and Shewanellaceae, respectively. Proteins involved in EET, such as the cytochromes PpcA and CymA, the outer membrane protein OmpJ, and the iron–sulfur cluster-binding CbcT, exhibited widespread distribution within Desulfovibrionaceae. Some of these showed modular diversification. Additional evidence revealed that horizontal gene transfer was involved in the acquiring and losing of critical genes, increasing the diversification and plasticity between the three families. The results suggest that specific EET genes were widely disseminated through horizontal transfer, where some changes reflected environmental adaptations. These findings enhance our comprehension of the evolution and distribution of proteins involved in EET processes, shedding light on their role in iron and sulfur biogeochemical cycling.

Sulfate reducing prokaryotes (SRP) are a phylogenetically and physiologically diverse group of microorganisms that use sulfate as an electron acceptor. SRP have long been recognized as key players of the carbon and sulfur cycles, and more recently, they have been identified to play a relevant role as part of syntrophic and symbiotic relations and the human microbiome. Despite their environmental relevance, there is a poor understanding about the prevalence of prophages and CRISPR arrays and how their distribution and dynamic affect the ecological role of SRP. We addressed this question by analyzing the results of a comprehensive survey of prophages and CRISPR in a total of 91 genomes of SRP with several genotypic, phenotypic, and physiological traits, including genome size, cell volume, minimum doubling time, cell wall, and habitat, among others. Our analysis discovered 81 prophages in 51 strains, representing the 56% of the total evaluated strains. Prophages are non-uniformly distributed across the SRP phylogeny, where prophage-rich lineages belonged to Desulfovibrionaceae and Peptococcaceae. Furthermore, our study found 160 CRISPR arrays in 71 SRP, which is more abundant and widely spread than previously expected. Although there is no correlation between presence and abundance of prophages and CRISPR arrays at the strain level, our analysis showed that there is a directly proportional relation between cellular volumes and number of prophages per cell. This result suggests that there is an additional selective pressure for strains with smaller cells to get rid of foreign DNA, such as prophages, but not CRISPR, due to less availability of cellular resources. Analysis of the prophage genes encoding viral structural proteins reported that 44% of SRP prophages are classified as Myoviridae, and comparative analysis showed high level of homology, but not synteny, among prophages belonging to the Family Desulfovibrionaceae. We further recovered viral-like particles and structures that resemble outer membrane vesicles from D. vulgaris str. Hildenborough. The results of this study improved the current understanding of dynamic interactions between prophages and CRISPR with their hosts in both cultured and hitherto-uncultured SRP strains, and how their distribution affects the microbial community dynamics in several sulfidogenic natural and engineered environments.

Parque Nacional La Campana (PNLC) is recognized worldwide for its flora and fauna, rather than for its microbial richness. Our goal was to characterize the structure and composition of microbial communities (bacteria, archaea and fungi) and their relationship with the plant communities typical of PNLC, such as sclerophyllous forest, xerophytic shrubland, hygrophilous forest and dry sclerophyllous forest, distributed along topoclimatic variables, namely, exposure, elevation and slope. The plant ecosystems, the physical and chemical properties of organic matter and the soil microbial composition were characterized by massive sequencing (iTag-16S rRNA, V4 and ITS1-5F) from the DNA extracted from the soil surface (5 cm, n = 16). A contribution of environmental variables, particularly related to each location, is observed. Proteobacteria (35.43%), Actinobacteria (32.86%), Acidobacteria (10.07%), Ascomycota (76.11%) and Basidiomycota (15.62%) were the dominant phyla. The beta diversity (~80% in its axes) indicates that bacteria and archaea are linked to their plant categories, where the xerophytic shrub stands out with the most particular microbial community. More specifically, Crenarchaeote, Humicola and Mortierella were dominant in the sclerophyllous forest; Chloroflexi, Cyanobacteria and Alternaria in the xerophytic shrubland; Solicoccozyma in the dry sclerophyllous forest; and Cladophialophora in the hygrophilous forest. In conclusion, the structure and composition of the microbial consortia is characteristic of PNLC’s vegetation, related to its topoclimatic variables, which suggests a strong association within the soil microbiome.

Coastal zones are ecosystems that are sensitive to climate change and anthropogenic pollution, resulting in a potential loss of biodiversity and ecosystem services through eutrophication and nutrient imbalances, among others. The coastal El Sauce catchment area, Central Chile, is under multiple anthropogenic pressures including wastewater treatment plant (WWTP) discharge, which its broad effect remains underexplored. In order to assess the impact of the WWTP on El Sauce stream, the benthic microbial communities and key functional groups variability (i.e., nitrifiers, methanogens and methanotrophs) were determined by 16S rDNA high-throughput sequencing and by functional genes quantification, respectively, during two contrasted seasons in three catchment areas (pre-, WWTP and post-discharge). The microbial communities’ structure profiles were associated with the water quality, nutrients, greenhouse gas (GHG) distribution, and the organic matter isotopic signatures in the sediments, for the first time, in this ecosystem. The results show that organic matter isotopic signatures using nitrogen and carbon (δ¹⁵N and δ¹³C) and the physicochemical conditions in El Sauce estuary changed from the pre- to WWTP discharge areas (i.e., a pH decrease of 0.5 units and an increase of 4–6 °C in the water temperature). The WWTP discharge area was characterized by a low nutrient concentration and significantly higher GHG distribution (>600 µM CO₂, >30,000 nM CH₄, and >3000 nM N₂O). In addition, the benthic microbial community structure shifted spatially and seasonally, including specific phyla known as sewage bioindicators, such as Firmicutes (Clostridiales order) and Bacteroidetes. In addition, other taxa were enriched or only retrieved in the sediments of the WWTP influenced area, e.g., Tenericutes, Lentisphaerae, Synergistetes, and LCP-89. Methanogens were more enriched near the WWTP discharge compared to those in the pre-discharge site in both seasons, while methanotrophs and ammonia oxidizers were unfavored only during winter. Our results indicate that the WWTP discharge impacts the biogeochemical conditions in El Sauce catchment area modifying the benthic microbial communities, including a decrease in the key functional groups able to mitigate CH₄ and regulate nutrients recycling in these aquatic ecosystems.