Mapping human pathogens in wastewater using a metatranscriptomic approach.

The monitoring of cities' wastewaters for the detection of potentially pathogenic viruses and bacteria has been considered a priority during the COVID-19 pandemic to monitor public health in urban environments. The methodological approaches frequently used for this purpose include deoxyribonucleic acid (DNA)/Ribonucleic acid (RNA) isolation followed by quantitative polymerase chain reaction (qPCR) and reverse transcription (RT)‒qPCR targeting pathogenic genes. More recently, the application of metatranscriptomic has opened opportunities to develop broad pathogenic monitoring workflows covering the entire pathogenic community within the sample. Nevertheless, the high amount of data generated in the process requires an appropriate analysis to detect the pathogenic community from the entire dataset. Here, an implementation of a bioinformatic workflow was developed to produce a map of the detected pathogenic bacteria and viruses in wastewater samples by analysing metatranscriptomic data. The main objectives of this work was the development of a computational methodology that can accurately detect both human pathogenic virus and bacteria in wastewater samples. This workflow can be easily reproducible with open-source software and uses efficient computational resources. The results showed that the used algorithms can predict potential human pathogens presence in the tested samples and that active forms of both bacteria and virus can be identified. By comparing the computational method implemented in this study to other state-of-the-art workflows, the implementation analysis was faster, while providing higher accuracy and sensitivity. Considering these results, the processes and methods to monitor wastewater for potential human pathogens can become faster and more accurate. The proposed workflow is available at https://github.com/waterpt/watermonitor and can be implemented in currently wastewater monitoring programs to ascertain the presence of potential human pathogenic species.

Exploration of the Types of Rarity in the Arctic Ocean from the Perspective of Multiple Methodologies.

The Arctic Ocean is facing rapid environmental changes with cascading effects on the entire Arctic marine ecosystem. However, we have a limited understanding of the consequences such changes have on bacteria and archaea (prokaryotes) at the base of the marine food web. In this study, we show how the prokaryotic rare biosphere behaves over a range of highly heterogeneous environmental conditions using 16S rRNA gene reads from amplicon and metagenome sequencing data from seawater samples collected during the Norwegian young sea ICE expedition between late winter and early summer. The prokaryotic rare biosphere was analyzed using different approaches: amplicon sequence variants and operational taxonomic units from the 16S rRNA gene amplicons and operational taxonomic units from the 16S rRNA genes of the metagenomes. We found that prokaryotic rare biosphere communities are specific to certain water masses, and that the majority of the rare taxa identified were always rare and disappeared in at least one sample under changing conditions, suggesting their high sensitivity to environmental heterogeneity. In addition, our methodological comparison revealed a good performance of 16S rRNA gene amplicon sequencing in describing rare biosphere patterns, while the metagenome-derived data were better to capture a significant diversity of so-far uncultivated rare taxa. Our analysis on the dynamics of the rare prokaryotic biosphere, by combining different methodological approaches, improves the description of the types of rarity predicted from Community Assembly theory in the Arctic Ocean.

The Extremophile Endolithella mcmurdoensis gen. et sp. nov. (Trebouxiophyceae, Chlorellaceae), A New Chlorella-like Endolithic Alga From Antarctica.

The McMurdo Dry Valleys constitute the largest ice-free region of Antarctica and one of the most extreme deserts on Earth. Despite the low temperatures, dry and poor soils and katabatic winds, some microbes are able to take advantage of endolithic microenvironments, inhabiting the pore spaces of soil and constituting photosynthesis-based communities. We isolated a green microalga, Endolithella mcmurdoensis gen. et sp. nov, from an endolithic sandstone sample collected in the McMurdo Dry Valleys (Victoria Land, East Antarctica) during the K020 expedition, in January 2013. The single non-axenic isolate (E. mcmurdoensis LEGE Z-009) exhibits cup-shaped chloroplasts, electron-dense bodies, and polyphosphate granules but our analysis did not reveal any diagnostic morphological characters. On the basis of phylogenetic analysis of the 18S rRNA (SSU) gene, the isolate was found to represent a new genus within the family Chlorellaceae.

Diversity and Composition of Pelagic Prokaryotic and Protist Communities in a Thin Arctic Sea-Ice Regime.

One of the most prominent manifestations of climate change is the changing Arctic sea-ice regime with a reduction in the summer sea-ice extent and a shift from thicker, perennial multiyear ice towards thinner, first-year ice. These changes in the physical environment are likely to impact microbial communities, a key component of Arctic marine food webs and biogeochemical cycles. During the Norwegian young sea ICE expedition (N-ICE2015) north of Svalbard, seawater samples were collected at the surface (5 m), subsurface (20 or 50 m), and mesopelagic (250 m) depths on 9 March, 27 April, and 16 June 2015. In addition, several physical and biogeochemical data were recorded to contextualize the collected microbial communities. Through the massively parallel sequencing of the small subunit ribosomal RNA amplicon and metagenomic data, this work allows studying the Arctic's microbial community structure during the late winter to early summer transition. Results showed that, at compositional level, Alpha- (30.7%) and Gammaproteobacteria (28.6%) are the most frequent taxa across the prokaryotic N-ICE2015 collection, and also the most phylogenetically diverse. Winter to early summer trends were quite evident since there was a high relative abundance of thaumarchaeotes in the under-ice water column in late winter while this group was nearly absent during early summer. Moreover, the emergence of Flavobacteria and the SAR92 clade in early summer might be associated with the degradation of a spring bloom of Phaeocystis. High relative abundance of hydrocarbonoclastic bacteria, particularly Alcanivorax (54.3%) and Marinobacter (6.3%), was also found. Richness showed different patterns along the depth gradient for prokaryotic (highest at mesopelagic depth) and protistan communities (higher at subsurface depths). The microbial N-ICE2015 collection analyzed in the present study provides comprehensive new knowledge about the pelagic microbiota below drifting Arctic sea-ice. The higher microbial diversity found in late winter/early spring communities reinforces the need to continue with further studies to properly characterize the winter microbial communities under the pack-ice.

Microbial response to a port fuel spill: Community dynamics and potential for bioremediation.

Following a fuel leakage inside a Portuguese maritime port, we conducted parallel 30-day experiments using contaminated seawater and fuel, sampled five days after the incident. This study aimed to (i)survey the native microbial community response to the spilled fuel and (ii)evaluate the efficacy of bioremediation, both biostimulation and bioaugmentation with a lyophilized bacterial consortium (Rhodococcus erythropolis, Pseudomonas sp.), in accelerating hydrocarbon degradation. Metabarcoding analysis revealed a shift in microbial communities, with increased abundance of hydrocarbon-degraders (e.g. Alcanivorax, Thalassospira). Ninety-five hydrocarbonoclastic bacteria were isolated, including key groups from the enriched communities. The lyophilized bacteria added in bioaugmentation, enhanced the abundance of hydrocarbon-degraders over time and were recovered throughout time. Bioremediation treatments favoured biodegradation, achieving over 60 % removal of total petroleum hydrocarbons after 15 days, contrasting with natural attenuation where almost no TPH was removed. This work highlights the potential of bioremediation technologies to accelerate hydrocarbon-degrading activity, for oil spills inside ports.

Sole microbiome progression in a hatchery life cycle, from egg to juvenile.

Recirculating aquaculture systems (RAS) pose unique challenges in microbial community management since they rely on a stable community with key target groups, both in the RAS environment and in the host (in this case, Solea senegalensis). Our goal was to determine how much of the sole microbiome is inherited from the egg stage, and how much is acquired during the remainder of the sole life cycle in an aquaculture production batch, especially regarding potentially probiotic and pathogenic groups. Our work comprises sole tissue samples from 2 days before hatching and up to 146 days after hatching (-2 to 146 DAH), encompassing the egg, larval, weaning, and pre-ongrowing stages. Total DNA was isolated from the different sole tissues, as well as from live feed introduced in the first stages, and 16S rRNA gene was sequenced (V6-V8 region) using the Illumina MiSeq platform. The output was analysed with the DADA2 pipeline, and taxonomic attribution with SILVAngs version 138.1. Using the Bray-Curtis dissimilarity index, both age and life cycle stage appeared to be drivers of bacterial community dissimilarity. To try to distinguish the inherited (present since the egg stage) from the acquired community (detected at later stages), different tissues were analysed at 49, 119 and 146 DAH (gill, intestine, fin and mucus). Only a few genera were inherited, but those that were inherited accompany the sole microbiome throughout the life cycle. Two genera of potentially probiotic bacteria (Bacillus and Enterococcus) were already present in the eggs, while others were acquired later, in particularly, forty days after live feed was introduced. The potentially pathogenic genera Tenacibaculum and Vibrio were inherited from the eggs, while Photobacterium and Mycobacterium seemed to be acquired at 49 and 119 DAH, respectively. Significant co-occurrence was found between Tenacibaculum and both Photobacterium and Vibrio. On the other hand, significantly negative correlations were detected between Vibrio and Streptococcus, Bacillus, Limosilactobacillus and Gardnerella. Our work reinforces the importance of life cycle studies, which can contribute to improve production husbandry strategies. However, we still need more information on this topic as repetition of patterns in different settings is essential to confirm our findings.

The impact of psychostimulants on central and peripheral neuro-immune regulation: a scoping review of cytokine profiles and their implications for addiction.

It is now well-accepted that psychostimulants act on glial cells causing neuroinflammation and adding to the neurotoxic effects of such substances. Neuroinflammation can be described as an inflammatory response, within the CNS, mediated through several cytokines, reactive oxygen species, chemokines and other inflammatory markers. These inflammatory players, in particular cytokines, play important roles. Several studies have demonstrated that psychostimulants impact on cytokine production and release, both centrally and at the peripheral level. Nevertheless, the available data is often contradictory. Because understanding how cytokines are modulated by psychoactive substances seems crucial to perspective successful therapeutic interventions, here, we conducted a scoping review of the available literature. We have focused on how different psychostimulants impact on the cytokine profile. Publications were grouped according to the substance addressed (methamphetamine, cocaine, methylphenidate, MDMA or other amphetamines), the type of exposure and period of evaluation (acute, short- or long-term exposure, withdrawal, and reinstatement). Studies were further divided in those addressing central cytokines, circulating (peripheral) levels, or both. Our analysis showed that the classical pro-inflammatory cytokines TNF-α, IL-6, and IL-1ß were those more investigated. The majority of studies have reported increased levels of these cytokines in the central nervous system after acute or repeated drug. However, studies investigating cytokine levels during withdrawal or reinstatement have shown higher variability in their findings. Although we have identified fewer studies addressing circulating cytokines in humans, the available data suggest that the results may be more robust in animal models than in patients with problematic drug use. As a major conclusion, an extensive use of arrays for relevant cytokines should be considered to better determine which cytokines, upon the classical ones, may be involved in the progression from episodic use to the development of addiction. A concerted effort is still necessary to address the link between peripheral and central immune players, including from a longitudinal perspective. Until there, the identification of new biomarkers and therapeutic targets to envision personalized immune-based therapeutics will continue to be unlikely.

Cadmium effects on net N2O production by the deep-sea isolate Shewanella loihica PV-4.

Deep-sea mining may lead to the release of high concentrations of metals into the surrounding seabed, which can disturb important ecosystem functions provided by microbial communities. Among these, the production of N2O and its reduction to N2 is of great relevance since N2O is an important greenhouse gas. Metal impacts on net N2O production by deep-sea bacteria are, however, currently unexplored. Here, we evaluated the effects of cadmium (Cd) on net N2O production by a deep-sea isolate, Shewanella loihica PV-4. We performed a series of Cd exposure incubations in oxic conditions and determined N2O fluxes during induced anoxic conditions, as well as the relative expression of the nitrite reductase gene (nirK), preceding N2O production, and N2O reductase gene (nosZ), responsible for N2O reduction. Net N2O production by S. loihica PV-4 exposed to Cd was strongly inhibited when compared to the control treatment (no metal). Both nirK and nosZ gene expression were inhibited in reactors with Cd, but nirK inhibition was stronger, supporting the lower net N2O production observed with Cd. The Cd inhibition of net N2O production observed in this study poses the question whether other deep-sea bacteria would undergo the same effects. Future studies should address this question as well as its applicability to complex communities and other physicochemical conditions, which remain to be evaluated.

Inter-comparison of marine microbiome sampling protocols.

Research on marine microbial communities is growing, but studies are hard to compare because of variation in seawater sampling protocols. To help researchers in the inter-comparison of studies that use different seawater sampling methodologies, as well as to help them design future sampling campaigns, we developed the EuroMarine Open Science Exploration initiative (EMOSE). Within the EMOSE framework, we sampled thousands of liters of seawater from a single station in the NW Mediterranean Sea (Service d'Observation du Laboratoire Arago [SOLA], Banyuls-sur-Mer), during one single day. The resulting dataset includes multiple seawater processing approaches, encompassing different material-type kinds of filters (cartridge membrane and flat membrane), three different size fractionations (>0.22 µm, 0.22-3 µm, 3-20 µm and >20 µm), and a number of different seawater volumes ranging from 1 L up to 1000 L. We show that the volume of seawater that is filtered does not have a significant effect on prokaryotic and protist diversity, independently of the sequencing strategy. However, there was a clear difference in alpha and beta diversity between size fractions and between these and "whole water" (with no pre-fractionation). Overall, we recommend care when merging data from datasets that use filters of different pore size, but we consider that the type of filter and volume should not act as confounding variables for the tested sequencing strategies. To the best of our knowledge, this is the first time a publicly available dataset effectively allows for the clarification of the impact of marine microbiome methodological options across a wide range of protocols, including large-scale variations in sampled volume.

The spatial distribution and biogeochemical drivers of nitrogen cycle genes in an Antarctic desert.

Antarctic deserts, such as the McMurdo Dry Valleys (MDV), represent extremely cold and dry environments. Consequently, MDV are suitable for studying the environment limits on the cycling of key elements that are necessary for life, like nitrogen. The spatial distribution and biogeochemical drivers of nitrogen-cycling pathways remain elusive in the Antarctic deserts because most studies focus on specific nitrogen-cycling genes and/or organisms. In this study, we analyzed metagenome and relevant environmental data of 32 MDV soils to generate a complete picture of the nitrogen-cycling potential in MDV microbial communities and advance our knowledge of the complexity and distribution of nitrogen biogeochemistry in these harsh environments. We found evidence of nitrogen-cycling genes potentially capable of fully oxidizing and reducing molecular nitrogen, despite the inhospitable conditions of MDV. Strong positive correlations were identified between genes involved in nitrogen cycling. Clear relationships between nitrogen-cycling pathways and environmental parameters also indicate abiotic and biotic variables, like pH, water availability, and biological complexity that collectively impose limits on the distribution of nitrogen-cycling genes. Accordingly, the spatial distribution of nitrogen-cycling genes was more concentrated near the lakes and glaciers. Association rules revealed non-linear correlations between complex combinations of environmental variables and nitrogen-cycling genes. Association rules for the presence of denitrification genes presented a distinct combination of environmental variables from the remaining nitrogen-cycling genes. This study contributes to an integrative picture of the nitrogen-cycling potential in MDV.

The microbial rare biosphere: current concepts, methods and ecological principles.

Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions and metabolic activity which make-up this communal pool, usually referred to as the 'rare biosphere', across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition and function.

To give or not to give antibiotics is not the only question.

In a 1945 Nobel Lecture, Sir Alexander Fleming warned against the overuse of antibiotics, particularly in response to public pressure. In the subsequent decades, evidence has shown that bacteria can become resistant to almost any available molecule. One key question is how the emergence and dissemination of resistant bacteria or resistance genes can be delayed. Although some clinicians remain sceptical, in this Personal View, we argue that the prescription of fewer antibiotics and shorter treatment duration is just as effective as longer regimens that remain the current guideline. Additionally, we discuss the fact that shorter antibiotic treatments exert less selective pressure on microorganisms, preventing the development of resistance. By contrast, longer treatments associated with a strong selective pressure favour the emergence of resistant clones within commensal organisms. We also emphasise that more studies are needed to identify the optimal duration of antibiotic therapy for common infections, which is important for making changes to the current guidelines, and to identify clinical biomarkers to guide antibiotic treatment in both hospital and ambulatory settings.

Secondary metabolite biosynthetic diversity in Arctic Ocean metagenomes.

Polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are mega enzymes responsible for the biosynthesis of a large fraction of natural products (NPs). Molecular markers for biosynthetic genes, such as the ketosynthase (KS) domain of PKSs, have been used to assess the diversity and distribution of biosynthetic genes in complex microbial communities. More recently, metagenomic studies have complemented and enhanced this approach by allowing the recovery of complete biosynthetic gene clusters (BGCs) from environmental DNA. In this study, the distribution and diversity of biosynthetic genes and clusters from Arctic Ocean samples (NICE-2015 expedition), was assessed using PCR-based strategies coupled with high-throughput sequencing and metagenomic analysis. In total, 149 KS domain OTU sequences were recovered, 36 % of which could not be assigned to any known BGC. In addition, 74 bacterial metagenome-assembled genomes were recovered, from which 179 BGCs were extracted. A network analysis identified potential new NP families, including non-ribosomal peptides and polyketides. Complete or near-complete BGCs were recovered, which will enable future heterologous expression efforts to uncover the respective NPs. Our study represents the first report of biosynthetic diversity assessed for Arctic Ocean metagenomes and highlights the potential of Arctic Ocean planktonic microbiomes for the discovery of novel secondary metabolites. The strategy employed in this study will enable future bioprospection, by identifying promising samples for bacterial isolation efforts, while providing also full-length BGCs for heterologous expression.

SARS-CoV-2 RNA detected in urban wastewater from Porto, Portugal: Method optimization and continuous 25-week monitoring.

Research on the emerging COVID-19 pandemic is demonstrating that wastewater infrastructures can be used as public health observatories of virus circulation in human communities. Important efforts are being organized worldwide to implement sewage-based surveillance of SARS-CoV-2 that can be used for preventive or early warning purposes, informing preparedness and response measures. However, its successful implementation requires important and iterative methodological improvements, as well as the establishment of standardized methods. The aim of this study was to develop a continuous monitoring protocol for SARS-CoV-2 in wastewater, that could be used to model virus circulation within the communities, complementing the current clinical surveillance. Specific objectives included (1) optimization and validation of a method for virus quantification; (2) monitoring the time-evolution of SARS-CoV-2 in wastewater from two wastewater treatment plants (WWTPs) in the city of Porto, Portugal. Untreated wastewater samples were collected weekly from the two WWTPs between May 2020 and March 2021, encompassing two COVID-19 incidence peaks in the region (mid-November 2020 and mid-January 2021). In the first stage of this study, we compared, optimized and selected a sampling and analysis protocol that included virus concentration through centrifugation, RNA extraction from both liquid and solid fractions and quantification by reverse transcription quantitative PCR (RT-qPCR). In the second stage, we used the selected methodology to track SARS-CoV-2 in the collected wastewater over time. SARS-CoV-2 RNA was detected in 39 and 37 out of 48 liquid and solid fraction samples of untreated wastewater, respectively. The copy numbers varied throughout the study between 0 and 0.15 copies/ng RNA and a good fit was observed between the SARS-CoV-2 RNA concentration in the untreated wastewater and the COVID-19 temporal trends in the study region. We also analyzed eight samples from the treated effluent and found no SARS-CoV-2 RNA detection after tertiary treatment and UV disinfection. In agreement with the recent literature, the results from this study support the use of wastewater-based surveillance to complement clinical testing and evaluate temporal and spatial trends of the current pandemic.

Depth Profile of Nitrifying Archaeal and Bacterial Communities in the Remote Oligotrophic Waters of the North Pacific.

Nitrification is a vital ecosystem function in the open ocean that regenerates inorganic nitrogen and promotes primary production. Recent studies have shown that the ecology and physiology of nitrifying organisms is more complex than previously postulated. The distribution of these organisms in the remote oligotrophic ocean and their interactions with the physicochemical environment are relatively understudied. In this work, we aimed to evaluate the depth profile of nitrifying archaea and bacteria in the Eastern North Pacific Subtropical Front, an area with limited biological surveys but with intense trophic transferences and physicochemical gradients. Furthermore, we investigated the dominant physicochemical and biological relationships within and between ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and nitrite-oxidizing bacteria (NOB) as well as with the overall prokaryotic community. We used a 16S rRNA gene sequencing approach to identify and characterize the nitrifying groups within the first 500 m of the water column and to analyze their abiotic and biotic interactions. The water column was characterized mainly by two contrasting environments, warm O2-rich surface waters with low dissolved inorganic nitrogen (DIN) and a cold O2-deficient mesopelagic layer with high concentrations of nitrate (NO3 -). Thaumarcheotal AOA and bacterial NOB were highly abundant below the deep chlorophyll maximum (DCM) and in the mesopelagic. In the mesopelagic, AOA and NOB represented up to 25 and 3% of the total prokaryotic community, respectively. Interestingly, the AOA community in the mesopelagic was dominated by unclassified genera that may constitute a novel group of AOA highly adapted to the conditions observed at those depths. Several of these unclassified amplicon sequence variants (ASVs) were positively correlated with NO3 - concentrations and negatively correlated with temperature and O2, whereas known thaumarcheotal genera exhibited the opposite behavior. Additionally, we found a large network of positive interactions within and between putative nitrifying ASVs and other prokaryotic groups, including 13230 significant correlations and 23 sub-communities of AOA, AOB, NOB, irrespective of their taxonomic classification. This study provides new insights into our understanding of the roles that AOA may play in recycling inorganic nitrogen in the oligotrophic ocean, with potential consequences to primary production in these remote ecosystems.

Bioremediation of Petroleum Hydrocarbons in Seawater: Prospects of Using Lyophilized Native Hydrocarbon-Degrading Bacteria.

This work aimed to develop a bioremediation product of lyophilized native bacteria to respond to marine oil spills. Three oil-degrading bacterial strains (two strains of Rhodococcus erythropolis and one Pseudomonas sp.), isolated from the NW Portuguese coast, were selected for lyophilization after biomass growth optimization (tested with alternative carbon sources). Results indicated that the bacterial strains remained viable after the lyophilization process, without losing their biodegradation potential. The biomass/petroleum ratio was optimized, and the bioremediation efficiency of the lyophilized bacterial consortium was tested in microcosms with natural seawater and petroleum. An acceleration of the natural oil degradation process was observed, with an increased abundance of oil-degraders after 24 h, an emulsion of the oil/water layer after 7 days, and an increased removal of total petroleum hydrocarbons (47%) after 15 days. This study provides an insight into the formulation and optimization of lyophilized bacterial agents for application in autochthonous oil bioremediation.

Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast.

Oil spills are among the most catastrophic events to marine ecosystems and current remediation techniques are not suitable for ecological restoration. Bioremediation approaches can take advantage of the activity of microorganisms with biodegradation capacity thus helping to accelerate the recovery of contaminated environments. The use of native microorganisms can increase the bioremediation efficiency since they have higher potential to survive in the natural environment while preventing unpredictable ecological impacts associated with the introduction of non-native organisms. In order to know the geographical scale to which a native bioremediation consortium can be applied, we need to understand the spatial heterogeneity of the natural microbial communities with potential for hydrocarbon degradation. In the present study, we aim to describe the genetic diversity and the potential of native microbial communities to degrade petroleum hydrocarbons, at an early stage of bioremediation, along the NW Iberian Peninsula coast, an area particularly susceptible to oil spills. Seawater samples collected in 47 sites were exposed to crude oil for 2 weeks, in enrichment experiments. Seawater samples collected in situ, and samples collected after the enrichment with crude oil, were characterized for prokaryotic communities by using 16S rRNA gene amplicon sequencing and predictive functional profiling. Results showed a drastic decrease in richness and diversity of microbial communities after the enrichment with crude oil. Enriched microbial communities were mainly dominated by genera known to degrade hydrocarbons, namely Alcanivorax, Pseudomonas, Acinetobacter, Rhodococcus, Flavobacterium, Oleibacter, Marinobacter, and Thalassospira, without significant differences between geographic areas and locations. Predictive functional profiling of the enriched microbial consortia showed a high potential to degrade the aromatic compounds aminobenzoate, benzoate, chlorocyclohexane, chlorobenzene, ethylbenzene, naphthalene, polycyclic aromatic compounds, styrene, toluene, and xylene. Only a few genera contributed for more than 50% of this genetic potential for aromatic compounds degradation in the enriched communities, namely Alcanivorax, Thalassospira, and Pseudomonas spp. This work is a starting point for the future development of prototype consortia of hydrocarbon-degrading bacteria to mitigate oil spills in the Iberian NW coast.

The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential.

Current research on the prokaryotic low abundance taxa, the prokaryotic rare biosphere, is growing, leading to a greater understanding of the mechanisms underlying organismal rarity and its relevance in ecology. From this emerging knowledge it is possible to envision innovative approaches in biotechnology applicable to several sectors. Bioremediation and bioprospecting are two of the most promising areas where such approaches could find feasible implementation, involving possible new solutions to the decontamination of polluted sites and to the discovery of novel gene variants and pathways based on the attributes of rare microbial communities. Bioremediation can be improved through the realization that diverse rare species can grow abundant and degrade different pollutants or possibly transfer useful genes. Further, most of the prokaryotic diversity found in virtually all environments belongs in the rare biosphere and remains uncultivatable, suggesting great bioprospecting potential within this vast and understudied genetic pool. This Mini Review argues that knowledge of the ecophysiology of rare prokaryotes can aid the development of future, efficient biotechnology-based processes, products and services. However, this promise may only be fulfilled through improvements in (and optimal blending of) advanced microbial culturing and physiology, metagenomics, genome annotation and editing, and synthetic biology, to name a few areas of relevance. In the future, it will be important to understand how activity profiles relate with abundance, as some rare taxa can remain rare and increase activity, whereas other taxa can grow abundant. The metabolic mechanisms behind those patterns can be useful in designing biotechnological processes.

The Response of Estuarine Ammonia-Oxidizing Communities to Constant and Fluctuating Salinity Regimes.

Aerobic nitrification is a fundamental nitrogen biogeochemical process that links the oxidation of ammonia to the removal of fixed nitrogen in eutrophicated water bodies. However, in estuarine environments there is an enormous variability of water physicochemical parameters that can affect the ammonia oxidation biological process. For instance, it is known that salinity can affect nitrification performance, yet there is still a lack of information on the ammonia-oxidizing communities behavior facing daily salinity fluctuations. In this work, laboratory experiments using upstream and downstream estuarine sediments were performed to address this missing gap by comparing the effect of daily salinity fluctuations with constant salinity on the activity and diversity of ammonia-oxidizing microorganisms (AOM). Activity and composition of AOM were assessed, respectively by using nitrogen stable isotope technique and 16S rRNA gene metabarcoding analysis. Nitrification activity was negatively affected by daily salinity fluctuations in upstream sediments while no effect was observed in downstream sediments. Constant salinity regime showed clearly higher rates of nitrification in upstream sediments while a similar nitrification performance between the two salinity regimes was registered in the downstream sediments. Results also indicated that daily salinity fluctuation regime had a negative effect on both ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) community's diversity. Phylogenetically, the estuarine downstream AOM were dominated by AOA (0.92-2.09%) followed by NOB (0.99-2%), and then AOB (0.2-0.32%); whereas NOB dominated estuarine upstream sediment samples (1.4-9.5%), followed by AOA (0.27-0.51%) and AOB (0.01-0.23%). Analysis of variance identified the spatial difference between samples (downstream and upstream) as the main drivers of AOA and AOB diversity. Our study indicates that benthic AOM inhabiting different estuarine sites presented distinct plasticity toward the salinity regimes tested. These findings help to improve our understanding in the dynamics of the nitrogen cycle of estuarine systems by showing the resilience and consequently the impact of different salinity regimes on the diversity and activity of ammonia oxidizer communities.

Understanding the Response of Nitrifying Communities to Disturbance in the McMurdo Dry Valleys, Antarctica.

Polar ecosystems are generally limited in nitrogen (N) nutrients, and the patchy availability of N is partly determined by biological pathways, such as nitrification, which are carried out by distinctive prokaryotic functional groups. The activity and diversity of microorganisms are generally strongly influenced by environmental conditions. However, we know little of the attributes that control the distribution and activity of specific microbial functional groups, such as nitrifiers, in extreme cold environments and how they may respond to change. To ascertain relationships between soil geochemistry and the ecology of nitrifying microbial communities, we carried out a laboratory-based manipulative experiment to test the selective effect of key geochemical variables on the activity and abundance of ammonia-oxidizing communities in soils from the McMurdo Dry Valleys of Antarctica. We hypothesized that nitrifying communities, adapted to different environmental conditions within the Dry Valleys, will have distinct responses when submitted to similar geochemical disturbances. In order to test this hypothesis, soils from two geographically distant and geochemically divergent locations, Miers and Beacon Valleys, were incubated over 2 months under increased conductivity, ammonia concentration, copper concentration, and organic matter content. Amplicon sequencing of the 16S rRNA gene and transcripts allowed comparison of the response of ammonia-oxidizing Archaea (AOA) and ammonia-oxidizing Bacteria (AOB) to each treatment over time. This approach was combined with measurements of 15NH4+ oxidation rates using 15N isotopic additions. Our results showed a higher potential for nitrification in Miers Valley, where environmental conditions are milder relative to Beacon Valley. AOA exhibited better adaptability to geochemical changes compared to AOB, particularly to the increase in copper and conductivity. AOA were also the only nitrifying group found in Beacon Valley soils. This laboratorial manipulative experiment provided new knowledge on how nitrifying groups respond to changes on key geochemical variables of Antarctic desert soils, and we believe these results offer new insights on the dynamics of N cycling in these ecosystems.