The Impact of Nitrogen-Fixing Bacteria-Based Biostimulant Alone or in Combination with Commercial Inoculum on Tomato Native Rhizosphere Microbiota and Production: An Open-Field Trial.

The agricultural sector is currently encountering significant challenges due to the effects of climate change, leading to negative consequences for crop productivity and global food security. In this context, traditional agricultural practices have been inadequate in addressing the fast-evolving challenges while maintaining environmental sustainability. A possible alternative to traditional agricultural management is represented by using beneficial micro-organisms that, once applied as bioinoculants, may enhance crop resilience and adaptability, thereby mitigating the adverse effects of environmental stressors and boosting productivity. Tomato is one of the most important crops worldwide, playing a central role in the human diet. The aim of this study was to evaluate the impact of a nitrogen-fixing bacterial-based biostimulant (Azospirillum sp., Azotobacter sp., and Rhizobium sp.) in combination or not with a commercial inoculum Micomix (Rhizoglomus irregulare, Funnelliformis mosseae, Funnelliformis caledonium, Bacillus licheniformis, and Bacillus mucilaginosus) (MYC) on the native rhizosphere communities and tomato production. Bacterial populations in the different samples were characterized using an environmental metabarcoding approach. The bioinocula effect on the native rhizosphere microbiota resulted in significant variation both in alpha and beta diversity and in a specific signature associated with the presence of biostimulants.

Microbial Ecology of Granular Biofilm Technologies for Wastewater Treatment: A Review.

Nowadays, the discharge of wastewater is a global concern due to the damage caused to human and environmental health. Wastewater treatment has progressed to provide environmentally and economically sustainable technologies. The biological treatment of wastewater is one of the fundamental bases of this field, and the employment of new technologies based on granular biofilm systems is demonstrating success in tackling the environmental issues derived from the discharge of wastewater. The granular-conforming microorganisms must be evaluated as functional entities because their activities and functions for removing pollutants are interconnected with the surrounding microbiota. The deep knowledge of microbial communities allows for the improvement in system operation, as the proliferation of microorganisms in charge of metabolic roles could be modified by adjustments to operational conditions. This is why engineering must consider the intrinsic microbiological aspects of biological wastewater treatment systems to obtain the most effective performance. This review provides an extensive view of the microbial ecology of biological wastewater treatment technologies based on granular biofilms for mitigating water pollution.

Rambellisea gigliensis and Rambellisea halocynthiae, gen. et spp. nov. (Lulworthiaceae) from the Marine Tunicate Halocynthia papillosa.

In this study, 15 Lulworthiales strains isolated from the marine tunicate Halocynthia papillosa collected in the central Tyrrhenian Sea were characterized using a polyphasic approach (morpho-physiological, molecular, and phylogenetic analyses). Based on multi-locus phylogenetic inference and morphological characters, a new genus, Rambellisea, and two new species, R. halocynthiae and R. gigliensis (Lulworthiales), were proposed. Multi-locus phylogenetic analyses using the nuclear ribosomal regions of DNA (nrITS1-nr5.8S-nrITS2, nrLSU, and nrSSU) sequence data strongly supported the new taxa. Phylogenetic inference, estimated using Maximum Likelihood and Bayesian Inference, clearly indicates that Rambellisea gen. nov. forms a distinct clade within the order Lulworthiales. Moreover, the two new species were separated into distinct subclades, solidly supported by the analyses. This is the first report of Lulworthiales species isolated from animals.

PGPB and/or AM Fungi Consortia Affect Tomato Native Rhizosphere Microbiota.

Tomatoes are one of the most important crops worldwide and also play a central role in the human diet. Microbial consortia are microorganism associations, often employed as bioinoculants, that can interact with the native rhizosphere microbiota. The aim of this study was to evaluate the impact of a bacterial-based biostimulant (Pseudomonas fluorescens and Bacillus amyloliquefaciens) (PSBA) in combination, or not, with a commercial inoculum Micomix (Rhizoglomus irregulare, Funnelliformis mosseae, Funnelliformis caledonium, Bacillus licheniformis, Bacillus mucilaginosus) (MYC) on the native rhizosphere communities and on tomato production. The trial was carried out using Solanum lycopersicum in an open field as follows: control full NPK (CFD), control reduced NPK (CRD), MYC, PSBA, PSBA + MYC. Bacterial population in the different samples were characterized using a next generation sequencing approach. The bioinocula effect on the native rhizosphere microbiota resulted in significant variation both in alpha and beta diversity and in a specific signature associated with the presence of biostimulants, especially in the presence of co-inoculation (PSBA + MYC). In particular, the high initial biodiversity shifts in the community composition occurred and consisted in the increase in the abundance of genera correlated to the soil acidification and in an enhanced density of nitrogen-fixing microbes. The results also highlighted the well-known rhizosphere effect.

Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench.

BACKGROUND: The Kuril-Kamchatka Trench (maximum depth 9604 m), located in the NW Pacific Ocean, is among the top seven deepest hadal trenches. The work aimed to investigate the unexplored abyssal-hadal prokaryotic communities of this fascinating, but underrated environment. RESULTS: As for the bacterial communities, we found that Proteobacteria (56.1-74.5%), Bacteroidetes (6.5-19.1%), and Actinobacteria (0.9-16.1%) were the most represented bacterial phyla over all samples. Thaumarchaeota (52.9-91.1%) was the most abundant phylum in the archaeal communities. The archaeal diversity was highly represented by the ammonia-oxidizing Nitrosopumilus, and the potential hydrocarbon-degrading bacteria Acinetobacter, Zhongshania, and Colwellia were the main bacterial genera. The α-diversity analysis evidenced that both prokaryotic communities were characterized by low evenness, as indicated by the high Gini index values (> 0.9). The ß-diversity analysis (Redundancy Analysis) indicated that, as expected, the depth significantly affected the structure of the prokaryotic communities. The co-occurrence network revealed seven prokaryotic groups that covaried across the abyssal-hadal zone of the Kuril-Kamchatka Trench. Among them, the main group included the most abundant archaeal and bacterial OTUs (Nitrosopumilus OTU A2 and OTU A1; Acinetobacter OTU B1), which were ubiquitous across the trench. CONCLUSIONS: This manuscript represents the first attempt to characterize the prokaryotic communities of the KKT abyssal-hadal zone. Our results reveal that the most abundant prokaryotes harbored by the abyssal-hadal zone of Kuril-Kamchatka Trench were chemolithotrophic archaea and heterotrophic bacteria, which did not show a distinctive pattern distribution according to depth. In particular, Acinetobacter, Zhongshania, and Colwellia (potential hydrocarbon degraders) were the main bacterial genera, and Nitrosopumilus (ammonia oxidizer) was the dominant representative of the archaeal diversity.

Impact of Plant-Beneficial Bacterial Inocula on the Resident Bacteriome: Current Knowledge and Future Perspectives.

The inoculation of plant growth-promoting bacteria (PGPB) as biofertilizers is one of the most efficient and sustainable strategies of rhizosphere manipulation leading to increased plant biomass and yield and improved plant health, as well as the ameliorated nutritional value of fruits and edible seeds. During the last decades, exciting, but heterogeneous, results have been obtained growing PGPB inoculated plants under controlled, stressful, and open field conditions. On the other hand, the possible impact of the PGPB deliberate release on the resident microbiota has been less explored and the little available information is contradictory. This review aims at filling this gap: after a brief description of the main mechanisms used by PGPB, we focus our attention on the process of PGPB selection and formulation and we provide some information on the EU regulation for microbial inocula. Then, the concept of PGPB inocula as a tool for rhizosphere engineering is introduced and the possible impact of bacterial inoculant on native bacterial communities is discussed, focusing on those bacterial species that are included in the EU regulation and on other promising bacterial species that are not yet included in the EU regulation.

Comparison of the Peel-Associated Epiphytic Bacteria of Anthocyanin-Rich "Sun Black" and Wild-Type Tomatoes under Organic and Conventional Farming.

Tomatoes are among the most consumed vegetables worldwide and represent a source of health-beneficial substances. Our study represents the first investigating the peel-associated epiphytic bacteria of red and purple (anthocyanin-rich) tomatoes subjected to organic and conventional farming systems. Proteobacteria was the dominant phylum (relative abundances 79-91%) in all experimental conditions. Enterobacteriaceae represented a large fraction (39.3-47.5%) of the communities, with Buttiauxella and Atlantibacter as the most represented genera. The core microbiota was composed of 59 operational taxonomic units (OTUs), including the majority of the most abundant ones. The occurrence of the most abundant OTUs differed among the experimental conditions. OTU 1 (Buttiauxella), OTU 2 (Enterobacteriales), and OTU 6 (Bacillales) were higher in red and purple tomatoes grown under organic farming. OTU 5 (Acinetobacter) had the highest abundance in red tomatoes subjected to organic farming. OTU 3 (Atlantibacter) was among the major OTUs in red tomatoes under both farming conditions. OTU 7 (Clavibacter) and OTU 8 (Enterobacteriaceae) had abundances ≥1% only in red tomatoes grown under conventional farming. PCA and clustering analysis highlighted a high similarity between the bacterial communities of red and purple tomatoes grown under organic farming. Furthermore, the bacterial communities of purple tomatoes grown under organic farming showed the lowest diversity and evenness. This work paves the way to understand the role of nutritional superior tomato genotypes, combined with organic farming, to modulate the presence of beneficial/harmful bacteria and supply healthier foods within a sustainable agriculture.

Could Pontimonas Harbour Halophilic Members Able to Withstand Very Broad Salinity Variations?

Pontimonas is currently described as a genus including only one species of slightly halophilic marine bacteria. Although some works revealed its presence in some hypersaline environments, the information on its habitat preference is still scant. This work investigated Pontimonas presence in selected ponds of the Saline di Tarquinia marine saltern and in the seawater intake area. The two-year metabarcoding survey documented its constant presence along the ponds establishing the salinity gradient and in a distinct basin with permanent hypersaline conditions (BSB). Pontimonas was higher in the ponds than in the sea, whereas it had similar abundances in the sea and in the BSB. Its representative OTUs showed significant trends according to different parameters. Along the salinity gradient, OTU1 abundance increased with decreasing water temperatures and increasing rainfalls, and it showed a maximum in January; OTU2 increased with increasing BOD5 and it showed the highest abundances in the period August-October, and OTU 3194 increased at decreasing salinities. In BSB, a significant seasonal variation was shown by OTU 3194, which started increasing in spring to reach a maximum in summer. The results suggest that Pontimonas could easily settle in hypersaline habitats, having also broad euryhaline members and some possible extreme halophilic representatives.

Polyextremophilic Chitinolytic Activity by a Marine Strain (IG119) of Clonostachys rosea.

The investigation for novel unique extremozymes is a valuable business for which the marine environment has been overlooked. The marine fungus Clonostachys rosea IG119 was tested for growth and chitinolytic enzyme production at different combinations of salinity and pH using response surface methodology. RSM modelling predicted best growth in-between pH 3.0 and 9.0 and at salinity of 0-40‱, and maximum enzyme activity (411.137 IU/L) at pH 6.4 and salinity 0‱; however, quite high production (>390 IU/L) was still predicted at pH 4.5-8.5. The highest growth and activity were obtained, respectively, at pH 4.0 and 8.0, in absence of salt. The crude enzyme was tested at different salinities (0-120‱) and pHs (2.0-13.0). The best activity was achieved at pH 4.0, but it was still high (in-between 3.0 and 12.0) at pH 2.0 and 13.0. Salinity did not affect the activity in all tested conditions. Overall, C. rosea IG119 was able to grow and produce chitinolytic enzymes under polyextremophilic conditions, and its crude enzyme solution showed more evident polyextremophilic features. The promising chitinolytic activity of IG119 and the peculiar characteristics of its chitinolytic enzymes could be suitable for several biotechnological applications (i.e., degradation of salty chitin-rich materials and biocontrol of spoiling organisms, possibly solving some relevant environmental issues).

Treatment of High-Polyphenol-Content Waters Using Biotechnological Approaches: The Latest Update.

Polyphenols and their intermediate metabolites are natural compounds that are spread worldwide. Polyphenols are antioxidant agents beneficial for human health, but exposure to some of these compounds can be harmful to humans and the environment. A number of industries produce and discharge polyphenols in water effluents. These emissions pose serious environmental issues, causing the pollution of surface or groundwater (which are used to provide drinking water) or harming wildlife in the receiving ecosystems. The treatment of high-polyphenol-content waters is mandatory for many industries. Nowadays, biotechnological approaches are gaining relevance for their low footprint, high efficiency, low cost, and versatility in pollutant removal. Biotreatments exploit the diversity of microbial metabolisms in relation to the different characteristics of the polluted water, modifying the design and the operational conditions of the technologies. Microbial metabolic features have been used for full or partial polyphenol degradation since several decades ago. Nowadays, the comprehensive use of biotreatments combined with physical-chemical treatments has enhanced the removal rates to provide safe and high-quality effluents. In this review, the evolution of the biotechnological processes for treating high-polyphenol-content water is described. A particular emphasis is given to providing a general concept, indicating which bioprocess might be adopted considering the water composition and the economic/environmental requirements. The use of effective technologies for environmental phenol removal could help in reducing/avoiding the detrimental effects of these chemicals. In addition, some of them could be employed for the recovery of beneficial ones.

Advances in Chitin and Chitosan Science.

Chitin is among the most abundant natural polysaccharides [...].

Spatio-Temporal Variation of the Bacterial Communities along a Salinity Gradient within a Thalassohaline Environment (Saline di Tarquinia Salterns, Italy).

The "Saline di Tarquinia" salterns have been scarcely investigated regarding their microbiological aspects. This work studied the structure and composition of their bacterial communities along the salinity gradient (from the nearby sea through different ponds). The communities showed increasing simplification of pond bacterial diversity along the gradient (particularly if compared to those of the sea). Among the 38 assigned phyla, the most represented were Proteobacteria, Actinobacteria and Bacteroidetes. Differently to other marine salterns, where at the highest salinities Bacteroidetes dominated, preponderance of Proteobacteria was observed. At the genus level the most abundant taxa were Pontimonas, Marivita, Spiribacter, Bordetella, GpVII and Lentibacter. The α-diversity analysis showed that the communities were highly uneven, and the Canonical Correspondence Analysis indicated that they were structured by various factors (sampling site, sampling year, salinity, and sampling month). Moreover, the taxa abundance variation in relation to these significant parameters were investigated by Generalized Linear Models. This work represents the first investigation of a marine saltern, carried out by a metabarcoding approach, which permitted a broad vision of the bacterial diversity, covering both a wide temporal span (two years with monthly sampling) and the entire salinity gradient (from the nearby sea up to the crystallisation ponds).

Vibrio communities along a salinity gradient within a marine saltern hypersaline environment (Saline di Tarquinia, Italy).

Vibrio species are ubiquitous in a number of different aquatic environments and promptly adapting to environmental changes due to high genome plasticity. The presence of these bacteria in marine salterns, in relation to a salinity gradient has been not investigated yet. Moreover, it is not clear if these hypersaline environments could represent a reservoir for Vibrio spp. This work investigated, through a metagenetic approach, the distribution of Vibrio (over 2 years) in different ponds along the salinity gradient within the 'Saline di Tarquinia' salterns, considering also the adjacent coastal waters and an isolated brine storage basin (BSB). Vibrio occurrence was higher in the sea than in the ponds and BSB, where it usually represented a rare taxon (abundance <1%). In the sea, it showed abundances in-between 1%-2.6% in 8 months out of 24. Four OTUs were assigned to the Vibrio genus; except for one that was more abundant in BSB, the others were much higher in the sea. Redundancy analysis (RDA) suggested a different distribution of the OTUs in relation to water temperature and salinity. Vibrio was found, even with low abundances, at the highest salinities also, suggesting the salterns as a possible reservoir for the bacterium.

Kinetic modeling of Shewanella baltica KB30 growth on different substrates through respirometry.

BACKGROUND: Shewanella baltica KB30 was isolated from seawater collected in Kandalaksha Bay, White Sea (Russia). This strain is known for its ability to grow on a pool of different substrates, including carbohydrates, carboxylic and amino acids, and lipids. However, no data are available on its metabolic efficiency in relation to the use of different carbon sources typologies. This work represents the first attempt to characterize S. baltica by its heterotrophic kinetic performance. RESULTS: Growth and substrate consumption, during the biodegradation of sodium acetate, glucose, tween 80 and peptone, were analyzed through a respirometric method. To find the model best fitting the experimental data and to obtain the kinetic parameters, the equations of Monod, Moser, Contois and Tessier were applied. The kinetic behavior of S. baltica was fitted to Monod model for sodium acetate and tween 80, while it was adjusted to Contois model for glucose and peptone. In this regard, peptone was consumed faster than the other substrates, as indicated by the highest values of substrate degradation rate, which exceeded 60 mg O2 L-1 h-1. CONCLUSIONS: Proteolytic metabolism was favored than lipidic and glucidic metabolism, which could contribute much more to mineralization and recycling of proteins than lipids and carbohydrates.

Evaluation of MALDI-TOF mass spectrometry and MALDI BioTyper in comparison to 16S rDNA sequencing for the identification of bacteria isolated from Arctic sea water.

MALDI-TOF Mass Spectrometry in association with the MALDI BioTyper 3.1 software has been evaluated for the identification and classification of 45 Arctic bacteria isolated from Kandalaksha Bay (White Sea, Russia). The high reliability of this method has been already demonstrated, in clinical microbiology, by a number of studies showing high attribution concordance with other credited analyses. Recently, it has been employed also in other branches of microbiology with controversial performance. The phyloproteomic results reported in this study were validated with those obtained by the "gold standard" 16S rDNA analysis. Concordance between the two methods was 100% at the genus level, while at the species level it was 48%. These percentages appeared to be quite high compared with other studies regarding environmental bacteria. However, the performance of MALDI BioTyper changed in relation to the taxonomical group analyzed, reflecting known identification problems related to certain genera. In our case, attribution concordance for Pseudomonas species was rather low (29%), confirming the problematic taxonomy of this genus, whereas that of strains from other genera was quite high (> 60%). Among the isolates tested in this study, two strains (Exiguobacterium oxidotolerans and Pseudomonas costantinii) were misidentified by MALDI BioTyper due to absence of reference spectra in the database. Accordingly, missing spectra were acquired for the database implementation.