Natural Bacterial Communities Research Articles

Impact of bacterial inoculations on Pisum sativum L. biometric parameters and associated bacterial and AM fungal communities under semi-arid field conditions in Tunisia

In Mediterranean agroecosystems, pea (Pisum sativum L.) is one important crop due to its nutritional benefits and high protein content. However, soil nutrient availability and soil health are known to affect pea productivity, especially under arid and semi-arid conditions. Currently, the use of plant growth-promoting bacteria (PGPB) may represent a bio-based tool to improve pea productivity in drought-affected areas. Nevertheless, there is limited knowledge on how PGPB inoculations in field could impact native communities of bacteria and arbuscular mycorrhizal fungi (AMF) in these areas. Here, a two-year field study in Tunisia was established to evaluate the effects of inoculating two pea varieties with three strains of potential PGPB, including Rhizobium laguerreae and two strains of Erwinia sp., on agronomic performance and soil microbial communities. Inoculations improved productivity and all measured biometric parameters, with the treatment including a consortia of the three strains showing the highest benefits. Metabarcoding analysis showed an increased bacterial and AM fungal diversity in soil of inoculated plants. Additionally, specific AMF-bacterial associations were identified, suggesting a synergistic role in enhancing soil health and pea growth. Overall, this study highlights the potential of targeted bacterial inoculations to improve pea performance under semi-arid environments by exploiting beneficial plant-microbe interactions. These results support the use of microbial inoculants as a sustainable agricultural practice in semi-arid areas, also improving the understanding of their impact on native bacterial and AM fungal communities.

Microbiome associated to an H2-emitting zone in the São Francisco basin Brazil

BackgroundDihydrogen (H₂) natural gas is a clean and renewable energy source of significant interest in the transition to sustainable energy. Unlike conventional petroleum-based fuels, H₂ releases only water vapor upon combustion, making it a promising alternative for reducing carbon footprints in the future. However, the microbial impact on H₂ dynamics in H2-emitting zones remains unclear, as does the origin of H2 — whether it is produced at greater depths or within shallow soil layers. In the São Francisco Basin, soil hydrogen concentrations of approximately 200 ppm were identified in barren ground depressions. In this study, we investigated the microbiome associated with this area using the 16S rRNA gene sequencing, with a focus on metabolic processes related to H₂ consumption and production. Soil samples were collected from two monitored (< 1 m) depths – 10 cm and 1 m – in the emission zone, which is predominantly covered with pasture vegetation, and from an adjacent area with medium and small trees.ResultsOur findings suggest that the H2-emitting zone significantly influences the composition and function of the microbiome, with Bacillus emerging as the dominant genus. In contrast to typical Cerrado soil, we observed a higher prevalence of Actinobacteriota (∼ 40%) and Firmicutes (∼ 20%). Additionally, we identified an abundance of sporulating bacteria and taxonomic groups previously described as H2-oxidizing bacteria.ConclusionsThe H2-emitting zone in the São Francisco Basin presents a unique opportunity to deepen our understanding of the impact of H₂ on microbial communities. This study is the first to characterize a natural H2-associated bacterial community in Cerrado soil using a culture-independent approach.

Mechanisms of microbial diversity modulation of mineral black clay to achieve ecological restoration of open-pit mine dump

The harsh climatic conditions and severe scarcity of surface soil present significant challenges to ecological restoration in open-pit mine dumps within China's type II plant cold resistance zone. To address the topsoil shortage, mineral black clay was used to create synthetic soil. This study explored the application of an ecological restoration bacteria (ERB) consortium to accelerate the ecological restoration of synthetic soil-covered areas by enhancing soil ecosystem construction. The results demonstrated that ERB significantly influenced the native bacterial community structure in mixed black clay. Specifically, ERB disrupted the inhibitory effects of the Actinobacterota phylum on the development of native bacterial diversity, leading to an increase in unclassified_o_Solirubrobacterales sp., norank_f_norank_o_norank_c_KD4-96 sp., Sphingomonas sp., Luteitalea sp., norank_f_Vicinamibacteraceae sp., and other aerobic and anaerobic bacteria. These alterations in soil microbial structure directly impacted soil composition and vegetation diversity. The plant diversity survey and metabolomics analysis revealed that the reduction of harmful substances, such as HPED, HODE, and HOME, in black clay soil improved the growth and distribution of Salsola collina Pall. and Medicago sativa L. This increase facilitated the cycling of key nutrients, such as nitrogen (N) and phosphorus (P), and promoted the establishment of symbiotic relationships between plants, microorganisms, and soil. Ultimately, the ecological remediation of the synthetic soil was achieved through the synergistic effects of ERB, which included the degradation of inhibitory soil components, enhanced nutrient consumption by microbiota and plants, and the overall promotion of ecosystem stability in the reclamation area.

Absence of synergistic effects between microplastics and copper ions on the spread of antibiotic resistance genes within aquatic bacteria at the community level

Microplastics and copper ions (Cu2+) are favorable in accelerating the propagation of antibiotic resistance genes (ARGs) in the plastisphere, however, their combined effects on the ARG spread within the bacterial community of the natural environment were less understood. The influence of microplastic types and Cu2+ concentrations on the horizontal gene transfer (HGT) of ARGs mediated by RP4 plasmid within natural bacterial communities in aquatic environments was investigated. Both biodegradable polybutylene succinate (PBS) and non-biodegradable polyvinyl chloride (PVC) microplastics significantly enhanced the transfer of ARGs, with PBS showing a significant higher effect compared to PVC. Cu2+ also increased transconjugation rates at environmentally relevant concentrations (5 μg L−1), but higher levels (50 μg L−1) lead to decreased rates due to severe bacterial cell membrane damage. The transconjugation rates in the presence of both microplastics and Cu2+ were lower than the sum of their individual effects, indicating no synergistic effects between them on transconjugation. Proteobacteria dominated the composition of transconjugates for all the treatment. Transmission electron microscope images and reactive oxygen species production in bacterial cells indicated that the increased contact frequency due to extracellular polymeric substances, combined with enhanced membrane permeability induced by microplastics and Cu2+, accounted for the increasing transconjugation rates. The study provides valuable insight into the potential effects of microplastics and heavy metals on the spread of ARGs from donors to bacterial communities in natural environments.

Parallel ecological and evolutionary responses to selection in a natural bacterial community

Evolution can occur over ecological timescales, suggesting a potentially important role for rapid evolution in shaping community trait distributions. However, evidence of concordant eco-evolutionary dynamics often comes from in vitro studies of highly simplified communities, and measures of ecological and evolutionary dynamics are rarely directly comparable. Here, we quantified how ecological species sorting and rapid evolution simultaneously shape community trait distributions by tracking within- and between-species changes in a key trait in a complex bacterial community. We focused on the production of siderophores; bacteria use these costly secreted metabolites to scavenge poorly soluble iron and to detoxify environments polluted with toxic nonferrous metals. We found that responses to copper-imposed selection within and between species were ultimately the same-intermediate siderophore levels were favored-and occurred over similar timescales. Despite being a social trait, this level of siderophore production was selected regardless of whether species evolved in isolation or in a community context. Our study suggests that evolutionary selection can play a pivotal role in shaping community trait distributions within natural, highly complex, bacterial communities. Furthermore, trait evolution may not always be qualitatively affected by interactions with other community members.

Investigating the interaction of uranium(VI) with diatoms and their bacterial community: A microscopic and spectroscopic study

Diatoms and bacteria play a vital role in investigating the ecological effects of heavy metals in the environment. Despite separate studies on metal interactions with diatoms and bacteria, there is a significant gap in research regarding heavy metal interactions within a diatom-bacterium system, which closely mirrors natural conditions. In this study, we aim to address this gap by examining the interaction of uranium(VI) (U(VI)) with Achnanthidium saprophilum freshwater diatoms and their natural bacterial community, primarily consisting of four successfully isolated bacterial strains (Acidovorax facilis, Agrobacterium fabrum, Brevundimonas mediterranea, and Pseudomonas peli) from the diatom culture. Uranium (U) bio-association experiments were performed both on the xenic A. saprophilum culture and on the four bacterial isolates. Scanning electron microscopy and transmission electron microscopy coupled with spectrum imaging analysis based on energy-dispersive X-ray spectroscopy revealed a clear co-localization of U and phosphorus both on the surface and inside A. saprophilum diatoms and the associated bacterial cells. Time-resolved laser-induced fluorescence spectroscopy with parallel factor analysis identified similar U(VI) binding motifs both on A. saprophilum diatoms and the four bacterial isolates. This is the first work providing valuable microscopic and spectroscopic data on U localization and speciation within a diatom-bacterium system, demonstrating the contribution of the co-occurring bacteria to the overall interaction with U, a factor non-negligible for future modeling and assessment of radiological effects on living microorganisms.

Substrate availability may limit the response of tropical bacterioplankton biomass to warming

AbstractThe response of heterotrophic bacterioplankton to the addition of macrophytic dissolved organic matter (DOM) and temperature was investigated in the Red Sea. We added 40 μmol C L−1 of leachates obtained from seagrass and mangrove leaves to natural bacterial communities, incubated them at three temperatures (25.5°C found in situ plus 3°C below and above that value) and monitored the microbial and biogeochemical responses over 4 d. Seagrass and mangrove DOM, important allochthonous sources in tropical oligotrophic regions, had distinct chemical characteristics compared to unamended seawater, with mangrove substrates containing comparatively more nitrogen and protein‐like fluorescent DOM than seagrass. Specific growth rates (μ) increased twofold in the seagrass and mangrove treatments (1.0 and 0.8 d−1, respectively) relative to the seawater control (0.4 d−1). The biomass of heterotrophic bacteria generally reflected μ changes, reaching maximum values of 16.8 and 17.3 μg C L−1 in the seagrass and mangrove treatments, respectively, compared to just 2.6 μg C L−1 in seawater. The increase in μ values due to experimental warming followed the metabolic theory of ecology, mostly because of enhanced exoenzymatic activity, while cell size decreased as predicted by the temperature–size rule (mean −3% per °C increase). Although the labile nature of the specific seagrass and mangrove DOM leachates was clearly demonstrated, we conclude that tropical heterotrophic bacteria may have limited capability to increase their biomass as a consequence of future warming, even in the presence of high loadings of macrophytic DOM.

Safeguarding reverse osmosis membrane integrity in drinking water production: A pilot study using 2 native bacterial communities and viruses in surface water as integrity indicators

Water treatment train including a reverse osmosis barrier is capable of producing high-quality water coupled with microbial safety. However, analytically proving this with log removal value (LRV) > 3 has remained a challenge. Conservative techniques that quantify salt or sulfate ion passage as virus surrogates are currently used to credit the membrane system for its microbial removal capacity. These methods are insensitive, and it is now understood that the transport mechanism correlation between these surrogates with the actual passage of viruses is weak. There is also a huge gap between the current log credit assigned (using spiking of surrogates in feed) and the actual log removal that can be proven in the drinking water plant. In this paper, we introduce two techniques that exploit the high concentration of microbial communities in fresh surface water by quantifying bacteria through flow cytometry (FC) and native viruses through qPCR assays. These two methods are compared to LRV of conductivity, TOC, and fluorescent markers. That high concentration of bacterial community allowed for LRV > 4 by flow cytometry in an intact module. After inflicting damage with a 1.5 mm defect, the FC method detected the damage, and a bacterial cell count >103 cell count/ml was measured in the permeate, while conductivity lacked sensitivity to monitor any integrity loss. Furthermore, after chlorine exposure to the membrane, both bacteria and virus detected no leakage, proving the membrane's intactness and also demonstrating the effect of chlorination on the passage of small solutes. The implementation of the two microbial quantifying methods in full-scale water treatment plants facilitates higher sensitivity in membrane integrity loss than currently used methods.

An inclusive study to elucidation the heavy metals-derived ecological risk nexus with antibiotic resistome functional shape of niche microbial community and their carbon substrate utilization ability in serpentine soil

Heavy metals (HMs) contained terrestrial ecosystems are often significantly display the antibiotic resistome in the pristine area due to increasing pressure from anthropogenic activity, is complex and emerging research interest. This study investigated that impact of chromium (Cr), nickel (Ni), cobalt (Co) concentrations in serpentine soil on the induction of antibiotic resistance genes and antimicrobial resistance within the native bacterial community as well as demonstrated their metabolic fingerprint. The full-length 16S-rRNA amplicon sequencing observed an increased abundance of Firmicutes, Actinobacteriota, and Acidobacteriota in serpentine soil. The microbial community in serpentine soil displayed varying preferences for different carbon sources, with some, such as carbohydrates and carboxylic acids, being consistently favored. Notably, 27 potential antibiotic resistance opportunistic bacterial genera have been identified in different serpentine soils. Among these, Lapillicoccus, Rubrobacter, Lacibacter, Chloroplast, Nitrospira, Rokubacteriales, Acinetobacter, Pseudomonas were significantly enriched in high and medium HMs concentrated serpentine soil samples. Functional profiling results illustrated that vancomycin resistance pathways were prevalent across all groups. Additionally, beta-lactamase, aminoglycoside, tetracycline, and vancomycin resistance involving specific bio-maker genes (ampC, penP, OXA, aacA, strB, hyg, aph, tet(A/B), otr(C), tet(M/O/Q), van(A/B/D), and vanJ) were the most abundant and enriched in the HMs-contaminated serpentine soil. Overall, this study highlighted that heavy-metal enriched serpentine soil is potential to support the proliferation of bacterial antibiotic resistance in native microbiome, and might able to spread antibiotic resistance to surrounding environment.

Genetically modified indigenous Pseudomonas aeruginosa drove bacterial community to change positively toward microbial enhanced oil recovery applications.

Microbial enhanced oil recovery (MEOR) is cost-effective and eco-friendly for oil exploitation. Genetically modified biosurfactants-producing high-yield strains are promising for ex-situ MEOR. However, can they survive and produce biosurfactants in petroleum reservoirs for in-situ MEOR? What is their effect on the native bacterial community? A genetically modified indigenous biosurfactants-producing strain Pseudomonas aeruginosa PrhlAB was bioaugmented in simulated reservoir environments. Pseudomonas aeruginosa PrhlAB could stably colonize in simulated reservoirs. Biosurfactants (200mg l-1) were produced in simulated reservoirs after bio-augmenting strain PrhlAB. The surface tension of fluid was reduced to 32.1 mN m-1. Crude oil was emulsified with an emulsification index of 60.1%. Bio-augmenting strain PrhlAB stimulated the MEOR-related microbial activities. Hydrocarbon-degrading bacteria and biosurfactants-producing bacteria were activated, while the hydrogen sulfide-producing bacteria were inhibited. Bio-augmenting P. aeruginosa PrhlAB reduced the diversity of bacterial community, and gradually simplified the species composition. Bacteria with oil displacement potential became dominant genera, such as Shewanella, Pseudomonas, and Arcobacter. Culture-based and sequence-based analyses reveal that genetically modified biosurfactants-producing strain P. aeruginosa PrhlAB are promising for in-situ MEOR as well.

The biological integrity of natural poly-species symbiotic bacterial communities for the production of kefir: Basic aspects of the preservation

An integral step in kefir production technology is the use of kefir grains, but in some cases it is necessary to maintain their population at the plant. A convenient method is freezing, but with direct freezing, kefir grains lose activity and some microorganisms die off. The use of substances with cryoprotective properties can help preserve kefir grains under direct freezing conditions. The study has examined three environments that have the potential to protect the symbiosis of kefir grains under subcryoscopic conditions: skim sterile milk, gelatin and a sterile solution of 30 % sucrose, and one environment that is stressful – sterile distilled water. At previous stages of research, it was proven that sharp defrosting aggravates the stress phenomena of the bacterial community, in particular, promotes the death of surface lactococci which leads to dysbacteriosis of the symbiosis. The work used for the first time a periodic scheme for defrosting kefir grains in a protective environment; the methods of visual and organoleptic assessment have been applied, the studies of microbiological and physico-chemical parameters of milk after fermentation of kefir starter with kefir grains have been conducted. Milk changes have been carried out using the technology of cultivating kefir grains with daily passages. It is accepted that if based on a set of indicators kefir grains from the experimental groups within 7 days correlate with the indicators detected for the control group, which was not subjected to freezing, then it is accepted that the kefir grains have completely restored viability. If this does not happen, a conclusion is drawn that the symbiosis has not been restored. As a result of the research, the prospects for using the studied substances as protective media have been proven and the need to construct specialized cryoprotective media for direct freezing of kefir grains in order to create your own kefir culture banks has been substantiated. The approach will reduce the use of bacterial substitutes for kefir like direct fermentation starters.

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.

Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities.

Most of Earth's trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth's land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew Pinus muricata plants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.IMPORTANCEUnderstanding how soil microbes interact with one another and their host plant will help us combat the negative effects that climate change has on terrestrial ecosystems. Unfortunately, we lack a clear understanding of how the presence of ectomycorrhizal fungi (EcMF)-one of the most dominant soil microbial groups on Earth-shapes belowground organic resources and the composition of bacterial communities. To address this knowledge gap, we profiled lipid and non-lipid metabolites in soils and plant roots, characterized soil bacterial communities, and compared soils amended either with or without EcMF. Our results show that the presence of EcMF changes soil organic resource availability, impacts the proliferation of different bacterial communities (in terms of both type and potential function), and primes plant root chemistry for pathogen suppression and energy conservation. Our findings therefore provide much-needed insight into how two of the most dominant soil microbial groups interact with one another and with their host plant.

Multi-biological risk in groundwater-surface water system under landfill stress: Driven by bacterial size and biological toxicity

The variation in bacterial size and biotoxicity leads to different ecological risks. However, the diversity of bacterial size and virulence in bacterial communities has been neglected, leading to limitations and inaccuracies in risk assessment. Surface-subsurface interactions lead to the complexity, variability, and insidiousness of pathogen transmission in the environment. Mountainous landfills are considered as a major source of pathogens in subsurface systems. Although numerous studies have reported the geographic distribution of microbes in landfills, there is a lack of knowledge regarding the impacts on the microbial spatial distribution of bacterial size, which is a key factor affecting microbial migration and risks. In this study, the groundwater, river water, soil and leachate samples were collected inside and around a typical mountainous urban landfill, which is close to a river with a high hydraulic gradient and a strong surface–subsurface interaction. Small-sized (<0.2 μm) and large-sized (>0.2 μm) bacteria were separated to verify the variability of migration potential and spatial distribution of different sizes of bacteria in groundwater-surface water and soil, investigating the driving factors and accessing the biological risk of different sizes of bacteria. The results revealed notable differences in spatial distribution and driving factors among various bacterial sizes. Small-sized bacterial communities in groundwater and soils exhibited clear trends towards leachate along the water flow direction. In contrast, large-sized bacterial communities remained stable and resembled native bacterial communities. Groundwater hydrodynamics was the main driving force affecting the spatial distribution of small-sized bacteria. The small-sized bacteria showed a higher content of virulence genes which were predominantly expressed for invasion. Thus, small-sized bacteria exhibited a stronger migration potential and a higher biological risk. Due to the surface–subsurface interactions, the bacterial communities in river water were more similar to that in groundwater after rain. Our results provide strong support to guide the management of subsurface system safety in mountainous landfills.

Bacterial diversity and functional characteristics of natural rainwater lakes in Saihanba artificial forest farm as revealed by 16S rRNA sequencing

The Saihanba Mechanical Forest is an artificial national forest park with a forest-steppe landscape. The flora and fauna have been extensively studied, but a comprehensive understanding of the bacterial community composition and structure of the natural rainwater lakes present in the area has rarely been reported. In this study, the structure and functional characteristics of bacterial communities in lake sediments and water samples in the Saihanba artificial forest were investigated using 16s rRNA high-throughput sequencing. Microbial diversity analyses revealed that Proteobacteria, Acidobacteria, Bacteroidota and Verrucomicrobiota microbiota dominated. The abundance of Proteobacteria and Actinobacteriota was significantly higher (p < .05) in water samples compared to sediment samples. PICRUSt2 functional analysis predicted genes associated with the degradation of xenobiotics and the execution of essential metabolic processes. Here, we report differences in the composition of native bacterial communities in sediments and water under the Saihanba artificial forest and make functional gene predictions. This study provides a reference for further exploring the structure and functional characteristics of microbial communities in water samples and sediment environments of lakes under planted forests.

Deciphering the interaction of bacteria inoculants with the recipient endophytic community in grapevine micropropagated plants.

Engineering the plant microbiome with beneficial endophytic bacteria can improve the growth, health, and productivity of the holobiont. Here, we administered two beneficial bacterial strains, Kosakonia VR04 sp. and Rhizobium GR12 sp., to micropropagated grapevine cuttings obtained via somatic embryogenesis. While both strains colonized the plant endosphere, only Rhizobium GR12 sp. increased root biomass under nutritional-deficit conditions, as supported by the plant growth promotion traits detected in its genome. Phylogenetic and co-occurrence analyses revealed that the plant native bacterial community, originally dominated by Streptococcaceae and Micrococcaceae, dramatically changed depending on the inoculation treatments, as invading strains differently affected the relative abundance and the interactions of pre-existing taxa. After 30 days of plantlets' growth, Pantoea became a predominant taxon, and considering untreated plantlets as references, Rhizobium sp. GR12 showed a minor impact on the endophytic bacterial community. On the other hand, Kosakonia sp. VR04 caused a major change in community composition, suggesting an opportunistic colonization pattern. Overall, the results corroborate the importance of preserving the native endophytic community structure and functions during plant microbiome engineering.IMPORTANCEA better comprehension of bacterial colonization processes and outcomes could benefit the use of plant probiotics in the field. In this study, we applied two different beneficial bacteria to grapevine micropropagated plantlets and described how the inoculation of these strains impacts endophytic microbiota assembly. We showed that under nutritional deficit conditions, the response of the receiving endophytic bacterial communities to the invasion of the beneficial strains related to the manifestation of plant growth promotion effects by the inoculated invading strains. Rhizobium sp. GR12 was able to preserve the native microbiome structure despite its effective colonization, highlighting the importance of the plant-endophyte associations for the holobiont performance. Moreover, our approach showed that the use of micropropagated plantlets could be a valuable strategy to study the interplay among the plant, its native microbiota, and the invader on a wider portfolio of species besides model plants, facilitating the application of new knowledge in agriculture.

Arsenic biomineralization and selenium nanoparticles biosynthesis by Halomonas boliviensis strain H-10 isolated from the high-altitude Salar de Huasco salt flat (Chile)

High-altitude Andean wetlands of the Atacama Desert (Chile), including the Salar de Huasco salt flat, are unusual environments characterized by a great variability of physical-chemical conditions, often combined with a high concentration of heavy metals, including arsenic (As) and semimetals, such as selenium (Se). Microorganisms present in these environments evolved adaptative strategies to cope with environmental stresses, with biotechnological potentials. The present work investigated the natural bacterial community composition in sediments collected from the Salar de Huasco salt flat, by high-throughput Illumina sequencing, and to isolate bacterial strains able to remove As and biosynthesize Se nanoparticles (SeNPs). Dominant taxonomic groups (abundance ≥1%) were affiliated to Proteobacteria (mainly consisting in Delta- and Alfa- Gamma-proteobacteria) Bacteriodetes, Firmicutes, Acidobacteria, Spirochaetes, Deinococcus-Thermus, Gemmatimonadetes and Verrucomicrobia. Halomonas boliviensis strain H-10 was able to both biomineralize As and biosynthesise SeNPs; therefore, the characteristics of H. boliviensis strain H-10 could be used for biotechnological purposes, including As bioremediation from water and bioproduction of SeNPs.

Bacterial degradation of ctenophore Mnemiopsis leidyi organic matter.

Blooms of gelatinous zooplankton, an important source of protein-rich biomass in coastal waters, often collapse rapidly, releasing large amounts of labile detrital organic matter (OM) into the surrounding water. Although these blooms have the potential to cause major perturbations in the marine ecosystem, their effects on the microbial community and hence on the biogeochemical cycles have yet to be elucidated. We conducted microcosm experiments simulating the scenario experienced by coastal bacterial communities after the decay of a ctenophore (Mnemiopsis leidyi) bloom in the northern Adriatic Sea. Within 24 h, a rapid response of bacterial communities to the M. leidyi OM was observed, characterized by elevated bacterial biomass production and respiration rates. However, compared to our previous microcosm study of jellyfish (Aurelia aurita s.l.), M. leidyi OM degradation was characterized by significantly lower bacterial growth efficiency, meaning that the carbon stored in the OM was mostly respired. Combined metagenomic and metaproteomic analysis indicated that the degradation activity was mainly performed by Pseudoalteromonas, producing a large amount of proteolytic extracellular enzymes and exhibiting high metabolic activity. Interestingly, the reconstructed metagenome-assembled genome (MAG) of Pseudoalteromonas phenolica was almost identical (average nucleotide identity >99%) to the MAG previously reconstructed in our A. aurita microcosm study, despite the fundamental genetic and biochemical differences of the two gelatinous zooplankton species. Taken together, our data suggest that blooms of different gelatinous zooplankton are likely triggering a consistent response from natural bacterial communities, with specific bacterial lineages driving the remineralization of the gelatinous OM.IMPORTANCEJellyfish blooms are increasingly becoming a recurring seasonal event in marine ecosystems, characterized by a rapid build-up of gelatinous biomass that collapses rapidly. Although these blooms have the potential to cause major perturbations, their impact on marine microbial communities is largely unknown. We conducted an incubation experiment simulating a bloom of the ctenophore Mnemiopsis leidyi in the Northern Adriatic, where we investigated the bacterial response to the gelatinous biomass. We found that the bacterial communities actively degraded the gelatinous organic matter, and overall showed a striking similarity to the dynamics previously observed after a simulated bloom of the jellyfish Aurelia aurita s.l. In both cases, we found that a single bacterial species, Pseudoalteromonas phenolica, was responsible for most of the degradation activity. This suggests that blooms of different jellyfish are likely to trigger a consistent response from natural bacterial communities, with specific bacterial species driving the remineralization of gelatinous biomass.

The interplay between Azospirillum brasilense and the native bacterial communities in the soil and rhizosphere of maize (Zea mays L.)

Azospirillum brasilense is a plant-growth promoting bacteria used as a bioinoculant in agriculture. However, the capacity of A. brasilense to establish itself in the soil and rhizosphere of different plants, as well as its interactions with the native soil bacterial community, are not fully understood. This knowledge gap can be attributed to inconsistencies in the quantity of the inoculant delivered (population size) and abiotic and biotic factors that modulate its performance. In this study, our objective was to gain a better understanding of how different-sized populations (sub-dose, recommended dose, and super-dose) of A. brasilense affect and interact with the structure, diversity, and connections of the native bacterial community in both bulk soil and rhizosphere of maize plants at different growth stages. Furthermore, we aimed to assess the effectiveness of these different-sized populations of A. brasilense in promoting plant growth. The introduction of a large population (recommended dose and super-dose) of A. brasilense significantly improved maize growth parameters, while a small population (sub-dose) did not. In the bulk soil, we observed that a large population of A. brasilense was capable of initially disrupt the native soil bacterial community. However, the native soil bacterial community was able to recover from the momentary disturbance and return to its initial state. In the rhizosphere of maize plants, large populations of A. brasilense extended their impact on the native bacterial community, possibly due to permanent changes in plant traits, such as root morphology and exudation. Furthermore, the co-occurrence network analysis revealed shifts in keystone taxa (i.e., taxa that confer high connectivity) in the rhizosphere of maize plants. A. brasilense played a key role at the early stages, but it was later replaced by Rhizobiales, a native soil bacterium. This study presents novel evidence of how different-sized populations of A. brasilense can influence microbe-microbe and plant-microbe interactions, ultimately affecting maize growth.

Surge of native rare taxa in tailings soil induced by peat bacterial invasion

The pivotal role of the native bacterial community in maintaining soil health, particularly in degraded tailings environments, is often overlooked. This study utilized peat, rich in microorganisms, to investigate its impact on soil function and native bacteria response in copper tailings-soil. Through 16S rRNA gene sequencing, changes in nutrient cycling, organic matter decomposition, and microbial activity were assessed post one-year peat remediation. Results from FEAST and cluster analysis revealed that peat-derived species disproportionately influenced tailings microbial community remediation, supported by the microbial invasion theory. Tailings responded positively to these species, with optimal function achieved at 5 % peat dosage. Peat biomarkers (Actinobacteriota, Bacteroida, Chloroflexi, and Firmicutes) played key roles in heavy metal removal and nutrition fixation. The Random Forest model and co-occurrence network highlighted contributions from native rare species (Dependentiae and Latescibacterota) activated by peat addition. These insights underscore the resilience of rare taxa and provide a foundation for soil health restoration in tailings areas. By emphasizing the importance of peat as a potential exogenous solution for activating indigenous microbial functions, these findings offer valuable insights for developing effective and sustainable remediation strategies in mining-affected regions.