Understanding the role of Francisella halioticida in mussel mortalities in France: an integrative approach.

Since 2014, mass mortalities of mussels Mytilus spp. have occurred in production areas on the Atlantic coast of France. The aetiology of these outbreaks remained unknown until the bacterium Francisella halioticida was detected in some mussel mortality cases. This retrospective study was conducted to assess the association between F. halioticida and these mussel mortalities. Mussel batches (n = 45) from the Atlantic coast and English Channel were selected from archived individual samples (n = 863) collected either during or outside of mortality events between 2014 and 2017. All mussels were analysed by real-time PCR assays targeting F. halioticida; in addition, 185 were analysed using histological analysis and 178 by 16S rRNA metabarcoding. F. halioticida DNA was detected by real-time PCR and 16S rRNA metabarcoding in 282 and 34 mussels, respectively. Among these individuals, 82% (real-time PCR analysis) and 76% (16S rRNA metabarcoding analysis) were sampled during a mortality event. Histological analyses showed that moribund individuals had lesions mainly characterized by necrosis, haemocyte infiltration and granulomas. Risk factor analysis showed that mussel batches with more than 20% of PCR-positive individuals were more likely to have been sampled during a mortality event, and positive 16S rRNA metabarcoding batches increased the strength of the association with mortality by 11.6 times. The role of F. halioticida in mussel mortalities was determined by reviewing the available evidence. To this end, a causation criteria grid, tailored to marine diseases and molecular pathogen detection tools, allowed more evidence to be gathered on the causal role of this bacterium in mussel mortalities.

Sequential oxidation-composting-phytoremediation treatment for the management of an oily sludge from petroleum refinery.

Oily sludges are generated in large quantities in petroleum refinery wastewater treatment plants. Given their complex composition, they are classified as hazardous waste. Selecting a single treatment technique for their remediation is challenging. This work aims to assess the extent of composting followed by phytoremediation on an oily sludge from an API separator unit, pre-treated by chemical oxidation with alkaline activated persulfate (PS). 18% of total petroleum hydrocarbons (TPH) were determined by IR spectroscopy. The aliphatic hydrocarbon content was 4714 ± 250 ppm by GC-FID, and aromatics were not detectable, suggesting a high amount of non-chromatographable complex hydrocarbons. The density of generalist and hydrocarbon-degrading populations of the oily sludge estimated by quantitative polymerase chain reaction (qPCR) evidenced an autochthonous microbiota with hydrocarbon-degrading capacity. The oxidative treatment with PS removed 31% of the TPH determined by IR after 20 days. The significant reduction of the native bacterial community was counterbalanced by coupling a composting treatment. Co-composting the sludge with goat manure and oat straw produced, after a year, a 96% reduction in TPH content, regardless of the oxidative pretreatment. Organic matter transformation was evidenced by the decrease of dissolved organic carbon (DOC) and the variation in E4/E6 ratio. The matrices obtained of composting were used as substrates for phytoremediation for 4 months. Ryegrass seeds were planted in both PS-treated and untreated sludge substrates. The presence of the plant grown in the pre-oxidised and composted substrate resulted in a higher aerial biomass of ryegrass (67%), an increase in enzymatic activities, and higher concentration of DOC, although without evidence of additional dissipation of TPH. The dynamics of the bacterial communities of the different substrates generated during the biological treatment were analyzed by Illumina NovaSeq DNA sequencing of 16S rRNA amplicons. The findings mirrored a succession compatible with that described in contaminated matrices, but also in other non-contaminated ones. According to these findings, an organic matter transformation process occurred, which included the complex hydrocarbons of the oily sludge, resulting in an active substrate that promoted the retention of nutrients and water and provided the necessary support for plant development.

Microbial community structure and metabolic profile of anthropized freshwater tributary channels from La Plata River, Argentina, to develop sustainable remediation strategies.

Microbial communities from freshwater sediments are involved in biogeochemical cycles and they can be modified by physical and chemical changes in the environment. Linking the microbial community structure (MCS) with physicochemistry of freshwater courses allows a better understanding of its ecology and can be useful to assess the ecological impact generated by human activity. The MCS of tributary channels from La Plata River affected by oil refinery (C, D, and E) and one also by urban discharges (C) was studied. For this purpose, 16S rRNA metabarcoding analysis, in silico metagenome functional prediction, and the hydrocarbon degradation potential (in silico predictions of hydrocarbon-degrading genes and their quantification by qPCR) of the MCS were studied. Principal coordinate analysis revealed that the MCS was different between sites, and it was not structured by the hydrocarbon content. Site C showed physicochemical characteristics, bacterial taxa, and an in silico functional prediction related to fermentative/heterotrophic metabolism. Site D, despite having higher concentration of hydrocarbon, presented autotrophic, syntrophic, and methanogenic pathways commonly involved in natural processes in anoxic sediments. Site E showed and intermediate autotrophic/heterotrophic behavior. The hydrocarbon degradation potential showed no positive correlation between the hydrocarbon-degrading genes quantified and predicted. The results suggest that the hydrocarbon concentration in the sites was not enough selection pressure to structure the bacterial community composition. Understanding which is the variable that structures the bacterial community composition is essential for monitoring and designing of sustainable management strategies for contaminated freshwater ecosystems.

Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect on Tomato Growth.

Mature composts and their water-based extracts, known as aerated compost teas (ACTs), are biofertilizers that share bioactive effects like soil restoration and plant health promotion, widely used for sustainable agriculture. Bioactive effects of compost and ACTs could be associated with their physicochemical and biological characteristics, like carbon/nitrogen (C/N) ratio and microbiota structure respectively. In our study, we elaborated ACTs using mature homemade compost, wheat bran, and grass clippings, following the C/N ratio criteria. Irrigation of tomato plantlets with ACT whose C/N ratio was close to the expected C/N ratio for mature compost evidenced plant growth promotion. Exploring the bacterial microbiota of elaborated ACTs and origin compost revealed significant structural differences, including phyla involved in N mineralization and free-living N-fixing bacteria. Therefore, ACTs harbor diverse bacterial microbiota involved in the N cycle, which would enrich plant and soil bacterial communities at the taxonomic and functional levels. Furthermore, ACTs are considered a part of agroecological and circular economy approaches.

Metabarcoding of colonic cleansing fluid reveals unique bacterial members of mucosal microbiota associated with Inflammatory Bowel Disease.

BACKGROUND: Inflammatory Bowel Disease (IBD) is a group of chronic idiopathic inflammatory diseases of the gastrointestinal (GI) tract associated with the dysbiosis of gut microbiota. Metabarcoding-based profiling of the gut microbiota of IBD patients is generally based on the stool samples collected from individual patients which rarely represent the mucosa-associated microbiota. The ideal sampling strategy for routine monitoring of the mucosal component of IBD has yet to be determined. METHODS: We hereby compare the microbiota composition of the colonic cleansing fluid (CCF) collected during colonoscopy with stool samples from IBD patients. The relationship between IBD and gut microbiota was revealed through the application of the 16S rRNA amplicon sequencing-based metabarcoding approach. CCF and stool samples were collected from IBD patients with Crohn's disease and ulcerative colitis. RESULTS: The present study shows significant differences in the microbial composition of CCF samples, presumably indicating changes in the mucosal microbiota of IBD patients as compared to the control group. Short-chain fatty acid-producing bacteria under the family Lachnospiraceae, the actinobacterial genus Bifidobacterium, the proteobacterial Sutterella and Raoultella are found to contribute to the microbial dysbiosis of the mucosal flora in IBD patients. CONCLUSIONS: CCF microbiota has the capacity to distinguish IBD patients from healthy controls and, thus, may constitute an alternative analysis strategy for the early diagnosis and disease progression in IBD biomarker research.

Metataxonomic characterization of the microbial community involved in the production of biogas with microcrystalline cellulose in pilot and laboratory scale.

Biogas, produced in anaerobic digestion, is a sustainable alternative for generating energy from agro-industrial and municipal waste. Information from the microbiota active in the process expands the possibilities for technological innovation. In this study, taxonomic annotations, and functional prediction of the microbial community of the inoculum of two processes were carried out: an industrial unit (pilot-scale urban solid waste plant-IU) and a laboratory-scale reactor fed with swine and cattle waste (LS). The biochemical potential of biogas was obtained using tested inoculum with microcrystalline cellulose, obtaining 682 LN/kgVS (LSC-laboratory scale inoculum and microcrystalline cellulose), and 583 LN/kgVS (IUC-industrial unit inoculum and microcrystalline cellulose), which is equivalent to a recovery of 91.5% of total biogas to LSC. The phyla Synergistota and Firmicutes were more abundant in LS/LSC. In the IU/IUC (treatment of restaurant waste and customs seizures), there was a greater microbiological variety and a predominance of the Bacteroidota, Cloacimonadota, Firmicutes and Caldatribacteriota. The genus Methanosaeta predominated in the process, and it was possible to infer the genes (K01895, K00193 and K00625) related to acetoclastic pathway, as well as endoglucanases that are involved in the metabolism of cellulose (LSC). Terpenoids, polyketides, cofactors, and vitamin metabolism were higher in reactors that received different substrates (IU; IUC). The taxonomic and functional differences revealed the importance of determining the microbiota in the analysis of the potential of an inoculum, combined with the use of microcrystalline cellulose, which can provide optimization information in the production of clean energy.

Oral ecological environment modifications by hard-cheese: from pH to microbiome: a prospective cohort study based on 16S rRNA metabarcoding approach.

BACKGROUND: The oral ecosystem conditions dental health, and is known to be positively modified by oral hygiene which cannot always be performed between meals, especially outside home. It is therefore important to identify the practices to be adopted to influence the oral environment in an anticariogenic direction. Milk and cheese are considered functional foods and have a role on oral health. There are several mechanisms by which cheese exerts its beneficial effects on teeth. The aim of the present study was to examine whether short term consumption of hard cheese would affect the oral pH and microbial flora of healthy adults modifying ecological oral environment. The Next Generation Sequencing (NGS) approach was applied to study the effect of Italian Grana Padano (GP), as a prototype of typical hard cheese, on the oral microbiota composition. Finally, we explored Streptococcus mutans/sanguinis ratio as a marker of protective biofilm composition. METHODS: Nine oral-healthy adults were instructed to eat 25 gr of GP cheese for 5 consecutive days. Three time points were chosen for supragingival samples collection and pH measurement. 16S rRNA-gene sequences were obtained both from oral samples and GP cheese using the MiSeq platform and analyzed against the expanded Human Oral Microbiome Database (eHOMD). ProgPerm was used to perform statistical analyses to investigate strain differential representation after cheese consumption. RESULTS: Taxonomic analyses of the oral microbiota revealed that Firmicutes was the most abundant phylum, followed by Proteobacteria and Actinobacteria. GP cheese significantly modifies oral pH, causing a shift toward basic conditions which are kept for a few hours. The Streptococcus mutans/Streptococcus sanguinis ratio lowers in the last observed timepoint. CONCLUSION: Our results reveal that a portion of GP cheese eaten after dinner provides important micronutrients (i.e. calcium, vitamins and some aminoacids such as arginine) and changes oral pH toward basic conditions, resulting in a light modification of the oral microbiome towards the reduction of the overall amount of acidophilic bacteria. Furthermore, the S. mutans/S. sanguinis ratio is reduced, contributing to obtain a more protecting environment towards caries establishment and evolution.

Evolution of prokaryotic colonisation of greenhouse plastics discarded into the environment.

Current knowledge on the capacity of plastics as vectors of microorganisms and their ability to transfer microorganisms between different habitats (i.e. air, soil and river) is limited. The objective of this study was to characterise the evolution of the bacterial community adhered to environmental plastics [low-density polyethylene (LDPE)] across different environments from their point of use to their receiving environment destination in the sea. The study took place in a typical Mediterranean intermittent river basin in Larnaka, Cyprus, characterised by a large greenhouse area whose plastic debris may end up in the sea due to mismanagement. Five locations were selected to represent the environmental fate of greenhouse plastics from their use, through their abandonment in soil and subsequent transport to the river and the sea, taking samples of plastics and the surrounding environments (soil and water). The bacterial community associated with each sample was studied by 16S rRNA metabarcoding; also, the main physicochemical parameters in each environmental compartment were analysed to understand these changes. The identification and chemical changes in greenhouse plastics were tracked using Attenuated Total Reflection Fourier Transform Infra-red spectroscopy (ATR-FTIR). Scanning Electron Microscope (SEM) analysis demonstrated an evolution of the biofilm at each sampling location. ß-diversity studies showed that the bacterial community adhered to plastics was significantly different from that of the surrounding environment only in samples taken from aqueous environments (freshwater and sea) (p-value p-value > 0.05). The environmental parameters (pH, salinity, total nitrogen and total phosphorus) explained the differences observed at each location to a limited extent. Furthermore, bacterial community differences among samples were lower in plastics collected from the soil than in plastics taken from rivers and seawater. Six genera (Flavobacterium, Altererythrobacter, Acinetobacter, Pleurocapsa, Georgfuchsia and Rhodococcus) were detected in the plastic, irrespective of the sampling location, confirming that greenhouse plastics can act as possible vectors of microorganisms between different environments: from their point of use, through a river system to the final coastal receiving environment. In conclusion, this study confirms the ability of greenhouse plastics to transport bacteria, including pathogens, between different environments. Future studies should evaluate these risks by performing complete sequencing metagenomics to decipher the functions of the plastisphere.

Long-Term Heat Selection of the Coral Endosymbiont Cladocopium C1acro (Symbiodiniaceae) Stabilizes Associated Bacterial Communities.

Heat-tolerant strains of the coral endosymbiont, Cladocopium C1acro (Symbiodiniaceae), have previously been developed via experimental evolution. Here, we examine physiological responses and bacterial community composition (using 16S rRNA gene metabarcoding) in cultures of 10 heat-evolved (SS) and 9 wild-type (WT) strains, which had been exposed for 6 years to 31 °C and 27 °C, respectively. We also examine whether the associated bacterial communities were affected by a three-week reciprocal transplantation to both temperatures. The SS strains had bacterial communities with lower diversities that showed more stability and lower variability when exposed to elevated temperatures compared with the WT strains. Amplicon sequence variants (ASVs) of the bacterial genera Labrenzia, Algiphilus, Hyphobacterium and Roseitalea were significantly more associated with the SS strains compared with the WT strains. WT strains showed higher abundance of ASVs assigned to the genera Fabibacter and Tropicimonas. We hypothesize that these compositional differences in associated bacterial communities between SS and WT strains also contribute to the thermal tolerance of the microalgae. Future research should explore functional potential between bacterial communities using metagenomics to unravel specific genomic adaptations.

Spatio-temporal dynamics of bacterial communities in the shoreline of Laurentian great Lake Erie and Lake St. Clair's large freshwater ecosystems.

BACKGROUND: Long-term trends in freshwater bacterial community composition (BCC) and dynamics are not yet well characterized, particularly in large lake ecosystems. We addressed this gap by temporally (15 months) and spatially (6 sampling locations) characterizing BCC variation in lakes Erie and St. Clair; two connected ecosystems in the Laurentian Great Lakes. RESULTS: We found a spatial variation of the BCC between the two lakes and among the sampling locations (significant changes in the relative abundance of 16% of the identified OTUs at the sampling location level). We observed five distinct temporal clusters (UPGMA broad-scale temporal variation) corresponding to seasonal variation over the 15 months of sampling. Temporal variation among months was high, with significant variation in the relative abundance of 69% of the OTUs. We identified significant differences in taxonomic composition between summer months of 2016 and 2017, with a corresponding significant reduction in the diversity of BCC in summer 2017. CONCLUSIONS: As bacteria play a key role in biogeochemical cycling, and hence in healthy ecosystem function our study defines the scope for temporal and spatial variation in large lake ecosystems. Our data also show that freshwater BCC could serve as an effective proxy and monitoring tool to access large lake health.

Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles.

Pollution affects most of the urban and forest environments at different levels causing well-known effects on human and plant health. The influence that pollutants exert on plant-associated microbiota might direct plant health and, in some cases, also the removal of pollutants by plants. With the advent of nanotechnologies, an increasing amount of engineered nanoparticles are being introduced into the environment, and consequently, their impact on plant-associated microorganisms needs to be investigated. In this context, silver nanoparticles (Ag-NPs) were experimentally supplied at leaf and root level of poplar plants to assess Ag-NPs effects on plant microbiota. Leaf Ag-NP treatment increased bacteria and fungi evenness and determined a significant reduction in both microbial groups, while root Ag-NP treatment reduced the bacterial and fungal biodiversity. Bioinformatics functional analysis showed that Ag-NP treatment reduced the aerobic and stimulated facultative anaerobic and oxidative stress-tolerant bacteria. Our study offers new insights into the effects of Ag-NPs on both phyllosphere and rhizosphere poplar-associated microbiota and may represent a first attempt to understand the behavior of microbial communities of a tree species growing in a polluted environment.

Comparative evaluation of analytical pipelines for illumina short- and nanopore long-read 16S rRNA gene amplicon sequencing with mock microbial communities.

Utility of a recently developed long-read pipeline, Emu, was assessed using an expectation-maximization algorithm for accurate read classification. We compared it to conventional short- and long-read pipelines, using well-characterized mock bacterial samples. Our findings highlight the necessity of appropriate data-processing for taxonomic descriptions, expanding our understanding of the precise microbiome.

Comparative analysis of microbiome inhabiting oxygenated and deoxygenated habitats using V3 and V6 metabarcoding of 16S rRNA gene.

We examine how oxygen levels and the choice of 16S ribosomal RNA (rRNA) tags impact marine bacterial communities using Next-Generation amplicon sequencing. Analyzing V3 and V6 regions, we assess microbial composition in both Oxygen minimum zones (OMZ) and non-OMZ (NOMZ) areas in the Arabian Sea (AS) and the Central Indian Ocean basin (CIOB) respectively. Operational taxonomic units (OTUs) at 97% similarity showed slightly higher richness and diversity with V6 compared to V3. Vertical diversity patterns were consistent across both regions. NOMZ showed greater richness and diversity than OMZ. AS and CIOB exhibited significant differences in bacterial community, diversity, and relative abundance at the order and family levels. Alteromonadaceae dominated the OMZ, while Pelagibacteraceae dominated the NOMZ. Synechococcaceae were found exclusively at 250 m in OMZ. Bacteria putatively involved in nitrification, denitrification, and sulfurylation were detected at both sites. Dissolved oxygen significantly influenced microbial diversity at both sites, while seasonal environmental parameters affected diversity consistently, with no observed temporal variation.

Culture-Dependent and Metabarcoding Characterization of the Sugar Beet (Beta vulgaris L.) Microbiome for High-Yield Isolation of Bacteria with Plant Growth-Promoting Traits.

The diversity of plant-associated bacteria is vast and can be determined by 16S rRNA gene metabarcoding. Fewer of them have plant-beneficial properties. To harness their benefits for plants, we must isolate them. This study aimed to check whether 16S rRNA gene metabarcoding has predictive power in identifying the majority of known bacteria with plant-beneficial traits that can be isolated from the sugar beet (Beta vulgaris L.) microbiome. Rhizosphere and phyllosphere samples collected during one season at different stages of plant development were analyzed. Bacteria were isolated on rich unselective media and plant-based media enriched with sugar beet leaves or rhizosphere extracts. The isolates were identified by sequencing the 16S rRNA gene and tested in vitro for their plant-beneficial properties (stimulation of germination; exopolysaccharide, siderophore, and HCN production; phosphate solubilization; and activity against sugar beet pathogens). The highest number of co-occurring beneficial traits was eight, found in isolates of five species: Acinetobacter calcoaceticus, Bacillus australimaris, B. pumilus, Enterobacter ludwiigi, and Pantoea ananatis. These species were not detected by metabarcoding and have not previously been described as plant-beneficial inhabitants of sugar beets. Thus, our findings point out the necessity of a culture-dependent microbiome analysis and advocate for low-nutrient plant-based media for high-yield isolation of plant-beneficial taxa with multiple beneficial traits. A culture-dependent and -independent approach is required for community diversity assessment. Still, isolation on plant-based media is the best approach to select isolates for potential use as biofertilizers and biopesticides in sugar beet cultivation.

Wild Avian Gut Microbiome at a Small Spatial Scale: A Study from a Mediterranean Island Population of Alectoris rufa.

This research is one of the few comparative descriptions at an intraspecific level of wild non-passerine microbiomes. We investigated for the first time the gut microbiome of red-legged partridges (Alectoris rufa) using fecal pellets in order to provide a more informed management. We focused on a small Italian population consisting of two demes (WEST, EAST) separated by about 20 km on the opposite sides of Elba Island. Given the small spatial scale, we set up a sampling protocol to minimize contamination from environmental bacteria, as well as differences due to variations in-among others-habitat, season, and age of feces, that could possibly affect the investigation of the three Elban sites. We found a significant divergence between the WEST and EAST Elban subpopulations in terms of microbial composition and alpha diversity. Although most represented bacterial phyla were the same in all the sites (Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes), microbiomes displayed a much higher diversity in western than in eastern partridges. This result might be related to locally diverging individual physiological needs and/or to different intensities in past releases of captive-bred birds between the two sides of Elba. We suggest that the two subpopulations should be treated as distinct management units.

Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing.

Metagenomics studies have revealed tremendous viral diversity in aquatic environments. Yet, while the genomic data they have provided is extensive, it is unannotated. For example, most phage sequences lack accurate information about their bacterial host, which prevents reliable phage identification and the investigation of phage-host interactions. This study aimed to take this knowledge further, using a viral metagenomic framework to decipher the composition and diversity of phage communities and to predict their bacterial hosts. To this end, we used water and sediment samples collected from seven sites with varying contamination levels in the Ebrié Lagoon in Abidjan, Ivory Coast. The bacterial communities were characterized using the 16S rRNA metabarcoding approach, and a framework was developed to investigate the virome datasets that: (1) identified phage contigs with VirSorter and VIBRANT; (2) classified these contigs with MetaPhinder using the phage database (taxonomic annotation); and (3) predicted the phages' bacterial hosts with a machine learning-based tool: the Prokaryotic Virus-Host Predictor. The findings showed that the taxonomic profiles of phages and bacteria were specific to sediment or water samples. Phage sequences assigned to the Microviridae family were widespread in sediment samples, whereas phage sequences assigned to the Siphoviridae, Myoviridae and Podoviridae families were predominant in water samples. In terms of bacterial communities, the phyla Latescibacteria, Zixibacteria, Bacteroidetes, Acidobacteria, Calditrichaeota, Gemmatimonadetes, Cyanobacteria and Patescibacteria were most widespread in sediment samples, while the phyla Epsilonbacteraeota, Tenericutes, Margulisbacteria, Proteobacteria, Actinobacteria, Planctomycetes and Marinimicrobia were most prevalent in water samples. Significantly, the relative abundance of bacterial communities (at major phylum level) estimated by 16S rRNA metabarcoding and phage-host prediction were significantly similar. These results demonstrate the reliability of this novel approach for predicting the bacterial hosts of phages from shotgun metagenomic sequencing data.

Culture and molecular methods as complementary tools for water quality management.

Bacterial communities in a full-scale drinking water treatment plant (DWTP) were characterized using matrix-assisted laser desorption/ionization time of flight mass-spectrometry (MALDI-TOF MS) to identify HPC isolates and the obtained results were compared to 16S rRNA (V4) metabarcoding data acquired in a previous study. Sixty-three samples were collected at nine stages of the potabilization process: river water and groundwater intake, decantation, sand filtration, ozonization, carbon filtration, reverse osmosis, the mixing chamber and post-chlorination drinking water. In total, 1807 bacterial colonies were isolated, 32 % of which were successfully identified to at least the genus level by MALDI-TOF MS using our previously developed Drinking Water Library. Trends in diversity were similar by both approaches, but differences were observed in the detection of taxa, especially at lower hierarchy levels. High bacterial diversity was observed in river and groundwater, where Proteobacteria predominated. The diversity decreased significantly after the chlorination step, where Bacillus sp. (Firmicutes) and an unknown genus of Obscuribacteraceae (Cyanobacteria) were the most prevalent genera according to MALDI-TOF MS and metabarcoding, respectively. The two approaches gave similar results for the decantation, sand filtration and mixing chamber steps, where the most abundant taxon was Flavobacterium. The combined use of these culture-based and culture-independent methods to characterize microbial populations may help to better understand the role of bacteria in water treatment and quality, which will be of value for DWTP management.

Novel Effects of Leonardite-Based Applications on Sugar Beet.

The present study aimed to explore the effects of foliar application of a leonardite-based product on sugar beet (Beta vulgaris L.) plants grown in the field. The approach concerned the evaluation of the community compositional structure of plant endophytic bacteria through a metabarcoding approach, the expression level of a gene panel related to hormonal metabolism and signaling, and the main sugar beet productivity traits. Results indicated that plants treated with leonardite (dosage of 2,000 ml ha-1, dilution 1:125, 4 mg C l-1) compared with untreated ones had a significant increase (p < 0.05) in (i) the abundance of Oxalicibacterium spp., recognized to be an endophyte bacterial genus with plant growth-promoting activity; (ii) the expression level of LAX2 gene, coding for auxin transport proteins; and (iii) sugar yield. This study represents a step forward to advance our understanding of the changes induced by leonardite-based biostimulant in sugar beet.

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system.

BACKGROUND: Fish skin microbiomes are rarely studied in inland water systems, in spite of their importance for fish health and ecology. This is mainly because fish species distribution often covaries with other biotic and abiotic factors, complicating the study design. We tackled this issue in the northern part of the Jordan River system, in which a few fish species geographically overlap, across steep gradients of water temperature and salinity. RESULTS: Using 16S rRNA metabarcoding, we studied the water properties that shape the skin bacterial communities, and their interaction with fish taxonomy. To better characterise the indigenous skin community, we excluded bacteria that were equally abundant in the skin samples and in the water samples, from our analysis of the skin samples. With this in mind, we found alpha diversity of the skin communities to be stable across sites, but higher in benthic loaches, compared to other fish. Beta diversity was found to be different among sites and to weakly covary with the dissolved oxygen, when treated skin communities were considered. In contrast, water temperature and conductivity were strong factors explaining beta diversity in the untreated skin communities. Beta diversity differences between co-occurring fish species emerged only for the treated skin communities. Metagenomics predictions highlighted the microbiome functional implications of excluding the water community contamination from the fish skin communities. Finally, we found that human-induced eutrophication promotes dysbiosis of the fish skin community, with signatures relating to fish health. CONCLUSIONS: Consideration of the background water microbiome when studying fish skin microbiomes, across varying fish species and water properties, exposes patterns otherwise undetected and highlight among-fish-species differences. We suggest that sporadic nutrient pollution events, otherwise undetected, drive fish skin communities to dysbiosis. This finding is in line with a recent study, showing that biofilms capture sporadic pollution events, undetectable by interspersed water monitoring. Video abstract.

Ecological assessment of groundwater ecosystems disturbed by recharge systems using organic matter quality, biofilm characteristics, and bacterial diversity.

Recharge of aquifers by urban stormwater may trigger significant ecological changes that can be detrimental to the biodiversity and functioning of groundwater ecosystems. Here, the effects of aquifer recharge (AR) on three levels of parameters were investigated: dissolved organic carbon (DOC) quantity and quality, global biofilm characteristics, and diversity changes of bacterial communities. As DOC enrichment by AR can be mitigated by vadose zone (VZ) thickness, three AR sites with thin VZ (< 3 m) and three sites with thick VZ (> 10 m) were selected. For each AR site, clay beads were incubated over a 10-day-long rainy period through wells in recharged and non-recharged groundwaters. Total proteins, dehydrogenase, and hydrolytic activities were monitored from clay beads to assess biofilm development. Bacterial richness on beads was estimated by 16S rRNA-based metabarcoding. AR was found to significantly increase DOC and biodegradable DOC (BDOC) concentrations, biofilm development, and bacterial richness especially in sites with thin VZ. VZ thickness was inversely related to microbial growth indicators and bacterial richness in groundwater, through a control of DOC availability. The proportion of Bacteroidetes 16S rRNA gene reads was higher in recharged groundwater than in non-recharged groundwater, suggesting that this phylum could be used as an indicator of DOC enrichment associated with AR. Quantitative PCR assays for Bacteroides DNA confirmed these trends and showed an enrichment of this bacterial group in DOC-rich aquifer waters. The positive linear relationships between BDOC concentrations and biofilm variables highlighted a strong C-limitation of groundwater impacting bacterial species sorting and activity.