Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes

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.

Microbial Biocontrol Agents and Natural Products Act as Salt Stress Mitigators in Lactuca sativa L

One of the major problems related to climate change is the increase in land area affected by higher salt concentrations and desertification. Finding economically and environmentally friendly sustainable solutions that effectively mitigate salt stress damage to plants is of great importance. In our work, some natural products and microbial biocontrol agents were evaluated for their long-term effectiveness in reducing salt stress in lettuce (Lactuca sativa L. var. romana) plants. Fourteen different treatments applied to soil pots, with and without salt stress, were analyzed using biometric (leaf and root length and width), physiological (chlorophyll and proline content), and morphological (microscopic preparations) techniques and NGS to study the microbial communities in the soil of plants subjected to different treatments. Under our long-term experimental conditions (90 days), the results showed that salt stress negatively affected plant growth. The statistical analysis showed a high variability in the responses of the different biostimulant treatments. Notably, the biocontrol agents Papiliotrema terrestris (strain PT22AV), Bacillus amyloliquefaciens (strain B07), and Rahnella aquatilis (strain 36) can act as salt stress mitigators in L. sativa. These findings suggest that both microbial biocontrol agents and certain natural products hold promise for reducing the adverse effects of salt stress on plants.

Urban stormwater green infrastructure: Evaluating the public health service role of bioretention using microbial source tracking and bacterial community analyses

Bioretention cells (BRCs) control stormwater flow on-site during precipitation, reducing runoff and improving water quality through chemical, physical, and biological processes. While BRCs are effective in these aspects, they provide habitats for wildlife and may face microbial hazards from fecal shedding, posing a potential threat to human health and the nearby environment. However, limited knowledge exists regarding the ability to control microbial hazards (e.g., beyond using typical indicator bacteria) through stormwater biofiltration. Therefore, the purpose of this study is to characterize changes in the bacterial community of urban stormwater undergoing bioretention treatment, with the goal of assessing the public health implications of these green infrastructure solutions. Samples from BRC inflow and outflow in Columbus, Ohio, were collected post-heavy storms from October 2021 to March 2022. Conventional culture-based E. coli monitoring and microbial source tracking (MST) were conducted to identify major fecal contamination extent and its sources (i.e., human, canine, avian, and ruminant). Droplet digital polymerase chain reaction (ddPCR) was utilized to quantify the level of host-associated fecal contamination in addition to three antibiotic resistant genes (ARGs): tetracycline resistance gene (tetQ), sulfonamide resistance gene (sul1), and Klebsiella pneumoniae carbapenemase resistance gene (blaKPC). Subsequently, 16S rRNA gene sequencing was conducted to characterize bacterial community differences between stormwater BRC inflow and outflow. Untreated urban stormwater reflects anthropogenic contamination, suggesting it as a potential source of contamination to waterbodies and urban environments. When comparing inlet and outlet BRC samples, urban stormwater treated via biofiltration did not increase microbial hazards, and changes in bacterial taxa and alpha diversity were negligible. Beta diversity results reveal a significant shift in bacterial community structure, while simultaneously enhancing the water quality (i.e., reduction of metals, total suspended solids, total nitrogen) of urban stormwater. Significant correlations were found between the bacterial community diversity of urban stormwater with fecal contamination (e.g. dog) and ARG (sul1), rainfall intensity, and water quality (hardness, total phosphorous). The study concludes that bioretention technology can sustainably maintain urban microbial water quality without posing additional public health risks, making it a viable green infrastructure solution for heavy rainfall events exacerbated by climate change.

Comparison of Bacterial Communities in Five Ectomycorrhizal Fungi Mycosphere Soil

Ectomycorrhizal fungi have huge potential value, both nutritionally and economically, but most of them cannot be cultivated artificially. To better understand the influence of abiotic and biotic factors upon the growth of ectomycorrhizal fungi, mycosphere soil and bulk soil of five ectomycorrhizal fungi (Calvatia candida, Russula brevipes, Leucopaxillus laterarius, Leucopaxillus giganteus, and Lepista panaeola) were used as research objects for this study. Illumina MiSeq sequencing technology was used to analyze the community structure of the mycosphere and bulk soil bacteria of the five ectomycorrhizal fungi, and a comprehensive analysis was conducted based on soil physicochemical properties. Our results show that the mycosphere soil bacteria of the five ectomycorrhizal fungi are slightly different. Escherichia, Usitatibacter, and Bradyrhizobium are potential mycorrhizal-helper bacteria of distinct ectomycorrhizal fungi. Soil water content, soil pH, and available potassium are the main factors shaping the soil bacterial community of the studied ectomycorrhizal fungi. Moreover, from the KEGG functional prediction and LEfSe analysis, there are significant functional differences not only between the mycosphere soil and bulk soil. 'Biosynthesis of terpenoidsand steroids', 'alpha-Linolenic acid metabolism', 'Longevity regulating pathway-multiple species', 'D-Arginine and D-ornithine metabolism', 'Nitrotoluene degradation' and other functions were significantly different in mycosphere soil. These findings have pivotal implications for the sustainable utilization of ectomycorrhizal fungi, the expansion of edible fungus cultivation in forest environments, and the enhancement of derived economic benefits.

Comparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter

Members of the genus Lysinibacillus attract attention for their mosquitocidal, bioremediation, and plant growth-promoting abilities. Despite this interest, comprehensive studies focusing on genomic traits governing plant growth and stress resilience in this genus using whole-genome sequencing are still scarce. Therefore, we sequenced and compared the genomes of three endophytic Lysinibacillus irui strains isolated from Canary Island date palms with the ex-type strain IRB4-01. Overall, the genomes of these strains consist of a circular chromosome with an average size of 4.6 Mb and a GC content of 37.2%. Comparative analysis identified conserved gene clusters within the core genome involved in iron acquisition, phosphate solubilization, indole-3-acetic acid biosynthesis, and volatile compounds. In addition, genome analysis revealed the presence of genes encoding carbohydrate-active enzymes, and proteins that confer resistance to oxidative, osmotic, and salinity stresses. Furthermore, pathways of putative novel bacteriocins were identified in all genomes. This illustrates possible common plant growth-promoting traits shared among all strains of L. irui. Our findings highlight a rich repertoire of genes associated with plant lifestyles, suggesting significant potential for developing inoculants to enhance plant growth and resilience. This study is the first to provide insights into the overall genomic signatures and mechanisms of plant growth promotion and biocontrol in the genus Lysinibacillus. KEY POINTS: • Pioneer study in elucidating plant growth promoting in L. irui through comparative genomics. • Genome mining identified biosynthetic pathways of putative novel bacteriocins. • Future research directions to develop L. irui-based biofertilizers for sustainable agriculture.

Devosia aquimaris sp. nov., isolated from seawater of the Changjiang River estuary of China

A gram-stain-negative, aerobic, rod-shaped bacterium strain CJK-A8-3T was isolated from a polyamine-enriched seawater sample collected from the Changjiang River estuary of China. The colonies were white and circular. Strain CJK-A8-3T grew optimally at 35 °C, pH 7.0 and 1.5% NaCl. Its polar lipids contained phosphatidylglycerol, phosphatidic acid, unidentified glycolipids, and a combination of phospholipids and glycolipids. The respiratory quinone was ubiquinone-10, and its main fatty acids were C16:0, 11-methyl C18:1ω7c and Summed Feature 8 (including C18:1ω7c/C18:1ω6c). The phylogenetic tree based on 16S rRNA genes placed strain CJK-A8-3T in a new linage within the genus Devosia. 16S rRNA gene sequence of strain CJK-A8-3T showed identities of 98.50% with Devosia beringensis S02T, 98.15% with D. oryziradicis, and 98.01% with D. submarina JCM 18935T. The genome size of strain CJK-A8-3T was 3.81 Mb with the DNA G + C content 63.9%, higher than those of the reference strains (60.4-63.8%). The genome contained genes functional in the metabolism of terrigenous aromatic compounds, alkylphosphonate and organic nitrogen, potentially beneficial for nutrient acquirement and environmental remediation. It also harbored genes functional in antibiotics resistance and balance of osmotic pressure, enhancing their adaptation to estuarine environments. Both genomic investigation and experimental verification showed that strain CJK-A8-3T could be versatile and efficient to use diverse organic nitrogen compounds as carbon and nitrogen sources. Based on phenotypic, chemotaxonomic, phylogenetic and genomic characteristics, strain CJK-A8-3T was identified as a novel Devosia species, named as Devosia aquimaris sp. nov. The type strain is CJK-A8-3T (= MCCC 1K06953T = KCTC 92162T).

Leveraging aquatic-terrestrial interfaces to capture putative habitat generalists

Habitat type is a strong determinant of microbial composition. Habitat interfaces, such as the boundary between aquatic and terrestrial systems, present unique combinations of abiotic factors for microorganisms to contend with. Aside from the spillover of certain harmful microorganisms from agricultural soils into water (e.g. fecal coliform bacteria), we know little about the extent of soil-water habitat switching across microbial taxa. In this study, we developed a proof-of-concept system to facilitate the capture of putatively generalist microorganisms that can colonize and persist in both soil and river water. We aimed to examine the phylogenetic breadth of putative habitat switchers and how this varies across different source environments. Microbial composition was primarily driven by recipient environment type, with the strongest phylogenetic signal seen at the order level for river water colonizers. We also identified more microorganisms colonizing river water when soil was collected from a habitat interface (i.e. soil at the side of an intermittently flooded river, compared to soil collected further from water sources), suggesting that environmental interfaces could be important reservoirs of microbial habitat generalists. Continued development of experimental systems that actively capture microorganisms that thrive in divergent habitats could serve as a powerful tool for identifying and assessing the ecological distribution of microbial generalists.

Enhanced mutualism: A promotional effect driven by bacteria during the early invasion of Phytolacca americana

The enhanced mutualism hypothesis postulates that invasive plants promote self-growth by enriching beneficial microbes to establish a positive soil feedback. However, the roles of soil microorganisms may vary with increasing time for plant growth. Research on changes in soil microbial communities over time has important implications for understanding the mechanisms underlying plant invasion. Due to the difficulty in evaluating the duration of plant growth, few studies have quantified the changes in soil microorganisms with increasing plant age. This study focuses on the invasive weed Phytolacca americana L., which has growth rings in the main root. We conducted a two-stage experiment in the field and greenhouse to explore the soil feedback changes with duration of plant growth. We determined the effects of P. americana at different ages on the soil microbial community and soil properties and performed a soil inoculation experiment to quantify the influence of soil microbes on seed germination and seedling performance. We found that the content of some soil nutrients, namely total nitrogen, total phosphorus, nitrate-N, and available phosphorus, significantly decreased with increasing growth age of P. americana, whereas the available potassium showed an opposite increasing trend. The P. americana growth age also significantly influenced the soil bacterial community structure. However, this phenomenon did not occur in the fungal community. In the bacterial community, the relative abundance of plant growth-promoting bacteria showed an increasing trend. The soil inoculation experiment had high seed germination rates and biomass accumulation when the plants were grown in conditioned soil from P. americana growth within 5 years, suggesting a positive plant-soil feedback. However, the promoting effect disappeared in conditioned soil from 10 years of age. Our findings demonstrate that plant growth-promoting bacteria significantly accumulated in the soil during the early stages of P. americana invasion, and that the strength of enhanced positive feedback may play a crucial role in facilitating P. americana invasion. This study highlights the changing nature of plant-microbe interactions during biological invasion and illustrates how bacteria could contribute to the initial success of P. americana, providing new insights into the underlying mechanisms of plant invasion.

Genotypic variation in grain cadmium concentration in wheat: Insights into soil pollution, agronomic characteristics, and rhizosphere microbial communities

Soil cadmium (Cd) pollution poses a serious threat to both the productivity and quality of wheat. This study aimed to investigate the genotypic variation in grain Cd concentration in wheat through field and pot experiments. Among 273 wheat genotypes, a significant genotypic difference was found in grain Cd concentration, ranging from 0.01 to 0.14 mg kg-1. Two contrasting genotypes, X321 (a low grain Cd accumulator) and X128 (a high grain Cd accumulator), were selected for pot experiments. X321 exhibited a 17.9% greater reduction in yield and a 10.2% lower shoot-to-grain Cd translocation rate than X128 under Cd treatment. Grain Cd content showed a positive correlation with soil available Cd content and a negative correlation with Cu content. Soil catalase activity significantly decreased in X128 under Cd stress, whereas no difference was found in X321. The grains of X321 exhibited a more compact spatial distribution of starch grains and protein matrix than those of X128. Moreover, the size of A-type starch in X128 was larger than in X321. Meanwhile, X128 contained much B-type starch, with some surface pits observed on A-type granules under Cd stress. Cd treatment increased the abundance of rhizosphere microorganism communities, with Ellin6067 and Ramlibacter being enriched in X128 under Cd treatment, which might facilitate Cd uptake. The accumulation of Cd in grains demonstrated a strong positive correlation with the rhizosphere bacterial diversity (correlation coefficient = 0.78). These findings provide new insights into the basis of grain Cd accumulation in wheat and have potential implications for developing new verities with low Cd accumulation to ensure food safety and minimize human exposure.

Indoor air VOCs biofiltration by bioactive coating packed bed bioreactors

Bioactive coatings are envisaged as a promising biotechnology to tackle the emerging problem of indoor air pollution. This solution could cope with the low concentrations, the wide range of compounds and the hydrophobicity of some indoor air VOCs, which are the most important bottlenecks regarding the implementation of conventional biotechnologies for indoor air treatment. A bioactive coating-based bioreactor was tested in this study for the abatement of different VOCs (n-hexane, toluene and α-pinene) at different empty bed residence times (EBRT) and inlet VOC concentrations. The performance of this reactor was compared with a conventional biofilm-based bioreactor operated with the same microbial inoculum. After an acclimation period, the bioactive coating-based bioreactor achieved abatements of over 50% for hexane, 80% for toluene and 70% for pinene at EBRTs of 112-56 s and inlet concentrations of 9-15 mg m-3. These results were about 25, 10 and 20% lower than the highest removals recorded in the biofilm-based bioreactor. Both bioreactors experienced a decrease in VOC abatement by ∼25% for hexane, 45% for toluene and 40% for pinene, after reducing the EBRT to 28 s. When inlet VOC concentrations were progressively reduced, VOC abatement efficiencies did not improve. This fact suggested that low EBRTs and low inlet VOCs concentration hindered indoor air pollutant abatement as a result of a limited mass transfer and bioavailability. Metagenomic analyses showed that process operation with toluene, hexane and pinene as the only carbon and energy sources favored an enriched bacterial community represented by the genera Devosia, Mesorhizobium, Sphingobacterium and Mycobacterium, regardless of the bioreactor configuration. Bioactive coatings were used in this work as packing material of a conventional bioreactor, achieving satisfactory VOC abatement similar to a conventional bioreactor.

Characterizing microbial communities associated with northern root-knot nematode (Meloidogyne hapla) occurrence and soil health

The northern root-knot nematode (Meloidogyne hapla) causes extensive damage to agricultural crops globally. In addition, M. hapla populations with no known genetic or morphological differences exhibit parasitic variability (PV) or reproductive potential based on soil type. However, why M. hapla populations from mineral soil with degraded soil health conditions have a higher PV than populations from muck soil is unknown. To improve our understanding of soil bio-physicochemical conditions in the environment where M. hapla populations exhibited PV, this study characterized the soil microbial community and core- and indicator-species structure associated with M. hapla occurrence and soil health conditions in 15 Michigan mineral and muck vegetable production fields. Bacterial and fungal communities in soils from where nematodes were isolated were characterized with high throughput sequencing of 16S and internal transcribed spacer (ITS) rDNA. Our results showed that M. hapla-infested, as well as disturbed and degraded muck fields, had lower bacterial diversity (observed richness and Shannon) compared to corresponding mineral soil fields or non-infested mineral fields. Bacterial and fungal community abundance varied by soil group, soil health conditions, and/or M. hapla occurrence. A core microbial community was found to consist of 39 bacterial and 44 fungal sub-operational taxonomic units (OTUs) across all fields. In addition, 25 bacteria were resolved as indicator OTUs associated with M. hapla presence or absence, and 1,065 bacteria as indicator OTUs associated with soil health conditions. Out of the 1,065 bacterial OTUs, 73.9% indicated stable soil health, 8.4% disturbed, and 0.4% degraded condition; no indicators were common to the three categories. Collectively, these results provide a foundation for an in-depth understanding of the environment where M. hapla exists and conditions associated with parasitic variability.

Exploration of potential driving mechanisms of Comamonas testosteroni in polycyclic aromatic hydrocarbons degradation and remodelled bacterial community during co-composting

Polycyclic aromatic hydrocarbons (PAHs) are a cluster of highly hazardous organic pollutants that are widespread in ecosystems and threaten human health. Composting has been shown to be an effective strategy for PAHs degredation. Here, we used Comamonas testosteroni as an inoculant in composting and investigated the potential mechanisms of PAHs degradation by co-occurrence network and structural equation modelling analysis. The results showed that more than 60% of PAHs were removed and the bacterial community responded to the negative effects of PAHs by upgrading the network. Inoculation with C. testosteroni altered bacterial community succession, intensified bacterial response to PAHs, improved metabolic activity, and promoted the degradation of PAHs during co-composting. The increased in the positive cohesion index of the community suggested that agents increased the cooperative behaviour between bacteria and led to changes in keystones of the bacterial network. However, the topological values of C. testosteroni in the network were not elevated, which confirmed that C. testosteroni altered communities by affecting other bacterial growth rather than its own colonisation. This study strengthens our comprehension of the potential mechanisms for the degradation of PAHs in inoculated composting.

Comparative Functional Genome Analysis Reveals the Habitat Adaptation and Biocontrol Characteristics of Plant Growth-Promoting Bacteria in NCBI Databases

Plant growth-promoting bacteria (PGPB) are a group of beneficial microorganisms that include 60 bacterial genera, such as Bacillus, Pseudomonas, and Burkholderia, which widely colonize plant leaves and soil, promote plant growth, and/or inhibit pathogen infection. However, the genetic factors underpinning adaptation of PGPB to plant leaves and soil remain poorly understood. In this study, we performed a comparative functional genome analysis approach to investigate the functional genes of 195 leaf-associated (LA) and 283 soil-associated (SA) PGPB strains and their roles in adapting to their environment, using 95 strains from other-associated (OA) environmental habitats with growth-promoting or antimicrobial functions as negative controls. Comparison analysis of the enrichment of nonredundant (NR) protein sequence databases showed that cytochrome P450, DNA repair, and motor chemotaxis genes were significantly enriched in LA PGPB strains related to environmental adaptation, while cell wall-degrading enzymes, TetR transcriptional regulatory factors, and sporulation-related genes were highly enriched in SA PGPB strains. Additionally, analysis of carbohydrate-active enzymes demonstrated that glycosyltransferases (GTs) and glycoside hydrolases (GHs) were abundant families in all PGPB strains, which is in favor of plant growth, and enriched in SA PGPB strains. Except for most Bacillus strains, SA PGPB genomes contained significantly more secondary metabolism clusters than LA PGPB. Most LA PGPB contained hormone biosynthesis genes, which may contribute to plant growth promotion, while SA PGPB harbored numerous carbohydrate and antibiotic metabolism genes. In summary, this study further deepens our understanding of the habitat adaptation and biocontrol characteristics of LA and SA PGPB strains. IMPORTANCE Plant growth-promoting bacteria (PGPB) are essential for the effectiveness of biocontrol agents in plant phyllosphere and rhizosphere. However, little is known about the ecological adaptation of PGPB to different habitats. In this study, comparative functional genome analysis of leaf-associated (LA), soil-associated (SA), and other-associated (OA) PGPB strains was performed. We found that genes related to the metabolism of hormones were enriched in LA PGPB. Carbohydrate and antibiotic metabolism genes were enriched in SA PGPB, which likely facilitated their adaptation to the plant growth environment. Our findings provide genetic insights on LA and SA PGPB strains' ecological adaptation and biocontrol characteristics.

Potential impacts of environmental bacteria on the microbiota of loggerhead (Caretta caretta) and green (Chelonia mydas) sea turtle eggs and their hatching success

Sea turtle hatching success can be affected by many variables, including pathogenic microbes, but it is unclear which microbes are most impactful and how they are transmitted into the eggs. This study characterized and compared the bacterial communities from the (i) cloaca of nesting sea turtles (ii) sand within and surrounding the nests; and (iii) hatched and unhatched eggshells from loggerhead (Caretta caretta) and green (Chelonia mydas) turtles. High throughput sequencing of bacterial 16S ribosomal RNA gene V4 region amplicons was performed on samples collected from 27 total nests in Fort Lauderdale and Hillsboro beaches in southeast Florida, United States. Significant differences were identified between hatched and unhatched egg microbiota with the differences caused predominately by Pseudomonas spp., found in higher abundances in unhatched eggs (19.29% relative abundance) than hatched eggs (1.10% relative abundance). Microbiota similarities indicate that the nest sand environment, particularly nest distance from dunes, played a larger role than the nesting mother's cloaca in influencing hatched and unhatched egg microbiota. Pathogenic bacteria potentially derive from mixed-mode transmission or additional sources not included in this study as suggested by the high proportion (24%-48%) of unhatched egg microbiota derived from unknown sources. Nonetheless, the results suggest Pseudomonas as a candidate pathogen or opportunistic colonizer associated with sea turtle egg-hatching failure.

Cell-free supernatant of Devosia sp. (strain SL43) mitigates the adverse effects of salt stress on soybean (Glycine max L.) seed vigor index

Soil salinity is a major constraint for soybean production worldwide, and the exploitation of plant growth-promoting bacteria (PGPB) and their bioactive metabolite(s) can improve plant salinity tolerance. With this objective, two experiments were performed, aiming to test 4 culture media (YEM(A), TYE(A), TS(A), and LB(A)) for growing a novel Devosia sp. (strain SL43), and then evaluating cell-free supernatants (CFS) from the Devosia sp. on germination of soybean (Glycine max L.) seeds under salinity stress. Soybean seeds were subjected to three salinity levels (0, 100, and 125 mM NaCl) and 6 levels of Devosia sp. CFS dilution (0, 1:1, 1:100, 1:250, 1:500, 1:1000). The results indicated that 125 mM NaCl concentration caused the greatest reduction in the total number of germinated seeds (15%), germination rate (43.6%), root length (55.2%), root weight (39.3%), and seed vigor (68%), and it also increased mean germination time by 71.9%. However, Devosia-CFS improved soybean germination, and the greatest effect was obtained at 1:1 dilution. Under the highest salinity level, application of CFS at 1:1 dilution increased final germination (17.6%), germination rate (18.6%), root length (162.2%), root weight (239.4%), seed vigor index (318.7%), and also shortening mean germination time by 19.2%. The results indicated that seed vigor index was positively correlated with other traits except for mean germination time. Our study suggested that the highest productivity of Devoisa sp. was obtained from the YEM medium. Results also suggested that CFS produced by the novel Devosia sp. (SL43 strain) can successfully alleviate salt stress effects on soybean seed germination and manipulating the chemical composition of the growth medium can influence the effectiveness of these bioactive metabolites.

Carbon Amendments Shape the Bacterial Community Structure in Salinized Farmland Soil

Practical, effective, and economically feasible salt reclamation and amelioration methods are in great demand in arid and semiarid areas. Energy amendments may be more appropriate than alternatives for improving salinized farmland soil because of their effects on soil microbes. We investigated the effects of biochar (Carbon) addition and desulfurization (noncarbon) on the soil bacterial community associated with Zea mays seedlings. Proteobacteria, Firmicutes, and Actinobacteriota were the dominant soil bacterial phyla. Biochar significantly increased soil bacterial biodiversity but desulfurization did not. The application of both amendments stimulated a soil bacterial community shift, and biochar amendments relieved selection pressure and increased the stochasticity of community assembly of bacterial communities. We concluded that biochar amendment can improve plant salt resistance by increasing the abundance of bacteria associated with photosynthetic processes and alter bacterial species involved in carbon cycle functions to reduce the toxicity of soil salinity to plants. IMPORTANCE Farmland application of soil amendments is a usual method to mitigate soil salinization. Most studies have concluded that soil properties can be improved by soil amendment, which indirectly affects the soil microbial community structures. In this study, we applied carbon and noncarbon soil amendments and analyzed the differences between them on the soil microbial community. We found that carbon soil amendment distinctly altered the soil microbial community. This finding provides key theoretical and technical support for using soil amendments in the future.

The long-acting herbicide mesosulfuron-methyl inhibits soil microbial community assembly mediating nitrogen cycling

Mesosulfuron-methyl is a widely used herbicide in wheat fields. We previously reported that mesosulfuron-methyl alters the bacterial/fungal community structure in experimental indoor microcosms, ultimately affecting NO₃^--N and NH₄⁺-N contents in soil nitrogen (N) cycling. However, how mesosulfuron-methyl application alter soil N cycling by changing microbial community assembly is unknown. Here, we designed an outdoor experiment comprising 2-month periods to investigate changes in soil N-cycle functional genes and structural shifts in the microbial community assembly in response to mesosulfuron-methyl applied at 11.25 and 112.5 g a.i. hm^-2. Results showed that high mesosulfuron-methyl input significantly decreased AOA amoA and nirK abundances within the initial 15 days, but increased AOB amoA on day 60. The nifH abundance displayed a stimulation-inhibition trend. Moreover, high mesosulfuron-methyl input decreased the network's complexity, and newly formed multiple network modules exhibited strong negative associations with nifH, AOB amoA, nirK and nirS. Further structural equation model demonstrated that mesosulfuron-methyl did reveal strong direct inhibition of nirK, and it indirectly affected nirK by changing nifH abundance and Planomicrobium. Thus mesosulfuron-methyl perturbs N-cycling processes by reshaping bacterial community assembly. Taken together, our study provides theoretical support for determining the microbiological mechanism by which mesosulfuron-methyl affects soil N cycling.

Single-cell Microbiomics Unveils Distribution and Patterns of Microbial Symbioses in the Natural Environment

Protist-bacteria associations are extremely common. Among them, those involving ciliates of the genus Euplotes are emerging as models for symbioses between prokaryotes and eukaryotes, and a great deal of information is available from cultured representatives of this system. Even so, as for most known microbial symbioses, data on natural populations is lacking, and their ecology remains largely unexplored; how well lab cultures represent actual diversity is untested. Here, we describe a survey on natural populations of Euplotes based on a single-cell microbiomic approach, focusing on taxa that include known endosymbionts of this ciliate. The results reveal an unexpected variability in symbiotic communities, with individual hosts of the same population harboring different sets of bacterial endosymbionts. Co-occurring Euplotes individuals of the same population can even have different essential symbionts, Polynucleobacter and "Candidatus Protistobacter," which might suggest that replacement events could be more frequent in nature than previously hypothesized. Accessory symbionts are even more variable: some showed a strong affinity for one host species, some for a sampling site, and two ("Candidatus Cyrtobacter" and "Candidatus Anadelfobacter") displayed an unusual pattern of competitive exclusion. These data represent the first insight into the prevalence and patterns of bacterial symbionts in natural populations of free-living protists.

Temporary establishment of bacteria from indoor plant leaves and soil on human skin

BACKGROUND

Plants are found in a large percentage of indoor environments, yet the potential for bacteria associated with indoor plant leaves and soil to colonize human skin remains unclear. We report results of experiments in a controlled climate chamber to characterize bacterial communities inhabiting the substrates and leaves of five indoor plant species, and quantify microbial transfer dynamics and residence times on human skin following simulated touch contact events. Controlled bacterial propagule transfer events with soil and leaf donors were applied to the arms of human occupants and repeatedly measured over a 24-h period using 16S rRNA gene amplicon sequencing.

RESULTS

Substrate samples had greater biomass and alpha diversity compared to leaves and baseline skin bacterial communities, as well as dissimilar taxonomic compositions. Despite these differences in donor community diversity and biomass, we observed repeatable patterns in the dynamics of transfer events. Recipient human skin bacterial communities increased in alpha diversity and became more similar to donor communities, an effect which, for soil contact only, persisted for at least 24 h. Washing with soap and water effectively returned communities to their pre-perturbed state, although some abundant soil taxa resisted removal through washing.

CONCLUSIONS

This study represents an initial characterization of bacterial relationships between humans and indoor plants, which represent a potentially valuable element of biodiversity in the built environment. Although environmental microbiota are unlikely to permanently colonize skin following a single contact event, repeated or continuous exposures to indoor biodiversity may be increasingly relevant for the functioning and diversity of the human microbiome as urbanization continues.

Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure

Sugarcane (Saccharum spp.) represents a crop of great economic importance, remarkably relevant in the food industry and energy supply chains from renewable sources. However, its conventional cultivation involves the intensive use of fertilizers, pesticides, and other agrochemical agents whose detrimental effects on the environment are notorious. Alternative systems, such as organic farming, have been presented as an environmentally friendly way of production. Still, the outcomes of different cropping systems on the microbiota associated with sugarcane-whose role in its health and growth is crucial-remain underexplored. Thus, we studied the rhizospheric microbiota of two adjacent sugarcane fields, which differ in terms of the type of farming system. For this, we used the sequencing of taxonomic markers of prokaryotes (gene 16S rRNA, subregions V3-V4) and fungi (Internal transcribed spacer 2) and evaluated the changes caused by the systems. Our results show a well-conserved microbiota composition among farming systems in the highest taxonomic ranks, such as phylum, class, and order. Also, both systems showed very similar alpha diversity indices and shared core taxa with growth-promoting capacities, such as bacteria from the Bacillus and Bradyrhizobium genera and the fungal genus Trichoderma. However, the composition at more specific levels denotes differences, such as the separation of the samples concerning beta diversity and the identification of 74 differentially abundant taxa between the systems. Of these, 60 were fungal taxa, indicating that this microbiota quota is more susceptible to changes caused by farming systems. The analysis of co-occurrence networks also showed the formation of peripheral sub-networks associated with the treatments-especially in fungi-and the presence of keystone taxa in terms of their ability to mediate relationships between other members of microbial communities. Considering that both crop fields used the same cultivar and had almost identical soil properties, we conclude that the observed findings are effects of the activities intrinsic to each system and can contribute to a better understanding of the effects of farming practices on the plant microbiome.

Interactions between Soil Bacterial Diversity and Plant-Parasitic Nematodes in Soybean Plants

Plant-parasitic nematodes are an important group of pests causing economic losses in agriculture worldwide. Among the plant-parasitic nematodes, the root-knot (Meloidogyne spp.) and root-lesion nematodes (Pratylenchus spp.) are considered the two most important ones affecting soybeans. In general, they damage soybean roots, causing a reduction of about one-third in productivity. The soil microbial community can exert a suppressive effect on the parasitism of plant-parasitic nematodes. Here, we investigated the effects of soil bacterial diversity on Meloidogyne javanica (Meloidogyne-assay) and Pratylenchus brachyurus (Pratylenchus-assay) suppression by manipulating microbial diversity using the dilution-to-extinction approach in two independent experiments under controlled conditions. Furthermore, we recorded the changes in the soil microbial community induced by plant-parasitic nematode infection. In Meloidogyne-assay, microbial diversity reduced the population density of M. javanica and improved plant performance. In Pratylenchus-assay, microbial diversity sustained the performance of soybean plants even at high levels of P. brachyurus parasitism. Each nematode population affected the relative abundance of different bacterial genera and altered the core microbiome of key groups within the bacterial community. Our findings provide fundamental insights into the interactions between soil bacterial diversity and plant-parasitic nematodes in soybean plants. IMPORTANCE Root-knot and root-lesion nematodes cause losses of billions of dollars every year to agriculture worldwide. Traditionally, they are controlled by using chemical nematicides, which in general have a negative impact on the environment and human health. Fortunately, the soil microbial community may suppress these pests, acting as an environmentally friendly alternative to control nematodes. However, the effects of soil microbial diversity on the parasitism of plant-parasitic nematodes still poorly understood. In this study, we provide fundamental insight into the interactions between soil bacterial diversity and plant-parasitic nematodes in soybean plants, which may be useful for the development of new strategies to control these phytopathogens.

A potential network structure of symbiotic bacteria involved in carbon and nitrogen metabolism of wood-utilizing insect larvae

Effective biological utilization of wood biomass is necessary worldwide. Since several insect larvae can use wood biomass as a nutrient source, studies on their digestive microbial structures are expected to reveal a novel rule underlying wood biomass processing. Here, structural inferences for inhabitant bacteria involved in carbon and nitrogen metabolism for beetle larvae, an insect model, were performed to explore the potential rules. Bacterial analysis of larval feces showed enrichment of the phyla Chroloflexi, Gemmatimonadetes, and Planctomycetes, and the genera Bradyrhizobium, Chonella, Corallococcus, Gemmata, Hyphomicrobium, Lutibacterium, Paenibacillus, and Rhodoplanes, as bacteria potential involved in plant growth promotion, nitrogen cycle modulation, and/or environmental protection. The fecal abundances of these bacteria were not necessarily positively correlated with their abundances in the habitat, indicating that they were selectively enriched in the feces of the larvae. Correlation and association analyses predicted that common fecal bacteria might affect carbon and nitrogen metabolism. Based on these hypotheses, structural equation modeling (SEM) statistically estimated that inhabitant bacterial groups involved in carbon and nitrogen metabolism were composed of the phylum Gemmatimonadetes and Planctomycetes, and the genera Bradyrhizobium, Corallococcus, Gemmata, and Paenibacillus, which were among the fecal-enriched bacteria. Nevertheless, the selected common bacteria, i.e., the phyla Acidobacteria, Armatimonadetes, and Bacteroidetes and the genera Candidatus Solibacter, Devosia, Fimbriimonas, Gemmatimonas Opitutus, Sphingobium, and Methanobacterium, were necessary to obtain good fit indices in the SEM. In addition, the composition of the bacterial groups differed depending upon metabolic targets, carbon and nitrogen, and their stable isotopes, δ¹³C and δ¹⁵N, respectively. Thus, the statistically derived causal structural models highlighted that the larval fecal-enriched bacteria and common symbiotic bacteria might selectively play a role in wood biomass carbon and nitrogen metabolism. This information could confer a new perspective that helps us use wood biomass more efficiently and might stimulate innovation in environmental industries in the future.

Management Practices Affecting Lesser Mealworm Larvae (Alphitobius diaperinus) Associated Microbial Community in a Broiler House and After Relocating With the Litter Into Pastureland

Lesser mealworms are often found infesting production houses used to raise broiler chickens. Previous studies have investigated pathogenic microorganisms associated with the larvae, but a more thorough study relating total microbiome changes due to management procedures and flock rotations was needed. Additionally, there is a question of what microbiota are transferred into the environment when the litter, in which larvae reside, is piled in pastureland for use as fertilizer and where interactions with the soil and other fauna can occur. This study chronicled, by the 16S rRNA sequencing, the bacterial community profile of larvae in a broiler grow-out house synchronizing to when birds were added to and removed from the house over 2.5 years. The profile was found to be relatively constant despite 11 flock rotations and management disruptions, specifically litter cleanout procedures and the addition of new birds or bedding. In contrast, once removed from the controlled broiler house environment and placed into open pastureland, the substantial microbial diversity brought with the larvae showed greater fluctuation in structure with environmental conditions, one of which was rainfall. Surprisingly, these larvae survived at least 19 weeks, so the potential for moving larval-associated microbes into the environment needs further assessment to minimize the risk of relocating foodborne pathogens and also to assess those bacteria-generating metabolites that have benefits to plant growth when using the litter as a fertilizer. The characterization of their microbiome is the first step to investigating the influences of their microbes on the manmade and environmental ecosystems.

The Deterioration of Agronomical Traits of the Continuous Cropping of Stevia Is Associated With the Dynamics of Soil Bacterial Community

Stevia rebaudiana Bertoni is grown worldwide as an important, natural sweetener resource plant. The yield of steviol glycosides (SVglys) is greatly influenced by continuous cropping. In this study, we collected the roots, rhizosphere soils, and bulk soils from 2 years of continuous cropping (Y2) and 8 years of continuous cropping (Y8). A high-throughput sequencing technology based on Illumina Hiseq 2500 platform was used to study the structure and diversity of bacterial communities in the roots and soils of stevia with different years of continuous cropping. The results demonstrated that although the content of a group of SVglys was significantly increased in stevia of long-term continuous cropping, it inhibited the growth of plants and lowered the leaf dry weight; as a result, the total amount of SVglys was significantly decreased. Meanwhile, continuous cropping changed the physicochemical properties and the bacterial composition communities of soil. The different sampling sources of the root, rhizosphere soil, and bulk soil had no impact on the richness of bacterial communities, while it exhibited obvious effects on the diversity of bacterial communities. Continuous cropping had a stronger effect on the bacterial community composition in rhizosphere soil than in root and bulk soil. Based on linear discriminant analysis effect size (LEfSe), in the rhizosphere soil of Y8, the relative abundance of some beneficial bacterial genera of Sphingomonas, Devosia, Streptomyces, and Flavobacterium decreased significantly, while the relative abundance of Polycyclovorans, Haliangium, and Nitrospira greatly increased. Moreover, the soil pH and nutrient content, especially the soil organic matter, were correlated with the relative abundance of predominant bacteria at the genus level. This study provides a theoretical basis for uncovering the mechanism of obstacles in continuous stevia cropping and provides guidance for the sustainable development of stevia.

Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India

Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on S cycling genes through metagenomic analysis of S contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio, and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment, and water were assigned to Proteobacteria as reflected from the reads per kilobase (RPKs) categorized into translation and ribosomal structure and biogenesis. An analysis of sequence similarity showed conserved pattern of both dsrAB genes (n = 178) retrieved from all metagenomes while other S disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of S oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, (i) the oxidative and reductive dsr evolutionary time-scale phylogeny proved that the earliest (but not the first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers, also we confirm that (ii) SRBs belongs to δ-Proteobacteria occurring independent lateral gene transfer (LGT) of dsr genes to different and few novel lineages. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score = 0.86, 0.98, 0.96) and Archaeoglobus fulgidus (TM score = 0.97, 0.98). We proposed that the genetic repertoire might provide the basis of studying time-scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling.

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. β-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.

Devosia salina sp. nov., isolated from South China Sea sediment

An aerobic, Gram-stain-negative, rod-shaped and motile strain, designated SCS-3T, was isolated from deep-sea sediment of the South China Sea. Phylogenetic analysis based on the 16S rRNA gene sequence similarities revealed that strain SCS-3T represented a novel species of the genus Devosia , with closely related strains ' Devosia sediminis ' MSA67T (98.61 %), Devosia riboflavina IFO13584T (98.22 %) and Devosia indica IO390501T (97.72 %). The G+C content of the genomic DNA is 63.44 mol%. The digital DNA–DNA hybridization values with ' D. sediminis ' MSA67T, D. riboflavina IFO13584T and D. indica IO390501T were 24.50, 21.8 and 24.80 %, respectively. The major polar lipids of strain SCS-3T were diphosphatidylglycerol, phosphatidylglycerol and three unidentified glycolipids. Ubiquinone-10 was the sole isoprenoid quinone, and C16 : 0, C18 : 1 ω7c 11-methyl and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c) were the major fatty acids. Based on polyphasic taxonomic data, strain SCS-3T represents a novel species of the genus Devosia , for which the name Devosia salina sp. nov. is proposed. The type strain is SCS-3T (=JCM 34403T=GDMCC 1.2221T).

Microbial community dynamics in the mesophilic and thermophilic phases of textile waste composting identified through next-generation sequencing

Composting is a promising source of mesophilic and thermophilic microorganisms directly involved in the decay of organic matter. However, there is a paucity of information related to bacterial and fungal diversity in compost and their enzymatic activities during the composting process. In this work, bacterial and fungal diversity during the mesophilic and thermophilic phases of textile waste composting was investigated as a way to explain the physical–chemical results obtained during the composting process. This was accomplished using a next-generation sequencing approach that targets either the 16S rRNA or ITS genomic regions of bacteria and fungi, respectively. It was observed that Proteobacteria, Bacteroidetes, and Actinobacteria were the dominant bacterial phyla present at the mesophilic phase but not at the thermophilic one. Composting textile waste exhibits a sustained thermophilic profile (above 55 °C) that usually precludes fungal activity. Nonetheless, the presence of fungi at the thermophilic phase was observed. Rozellomycota, Basidiomycota, and Ascomycota were the most dominant phyla during both composting phases. Such thermophilic fungi with great ability to decay organic matter could be isolated as pure cultures and used for the bioaugmentation of textile waste composting to achieve an advanced maturity level of textile waste compost.

Devosia rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., novel plant growth promoting members of the genus Devosia, isolated from the rhizosphere of rice plants

Two novel Gram-negative, aerobic, asporogenous, motile, rod-shaped, orange and white pigmented, designated as LEGU1^T and G19^T, were isolated from the roots of rice plants, collected from Goyang, South Korea. Phylogenetic analysis based on their 16S rRNA gene sequences revealed that they belonged to the genus Devosia and formed a different lineage and clusters with different members of the genus Devosia. These strains shared common chemotaxonomic features. In particular, they had Q-10 as the sole quinone, phosphatidylglycerol, diphosphatidylglycerol as the principal polar lipids and C_16:0, C_18:1ω7c 11-methyl and summed feature 8 (comprising C_18:1ω7c/C_18:1ω6c) as the main fatty acids. The draft genome sequences of strains LEGU1^T and G19^T were 3,524,978 and 3,495,520 bp in size, respectively. Their average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values were 72.8-81.9% and 18.7-25.1%, respectively, with each other and type strains of related species belonging to the genus Devosia, suggesting that these two strains represent novel species. The G + C content of strains LEGU1^T and G19^T were 62.1 and 63.8%, respectively. Of the two strains, only LEGU1^T produced carotenoid and flexirubin-type pigment. Both strains produced siderophore and indole acetic acid (IAA) in the presence of L-tryptophan. Siderophore biosynthesis genes, auxin responsive genes and tryptophan biosynthesis genes were present in their genomes. The present study aimed to determine the detailed taxonomic positions of the strains using the modern polyphasic approach. Based on the results of polyphasic analysis, these strains are suggested to be two novel bacterial species within the genus Devosia. The proposed names are D. rhizoryzae sp. nov., and Devosia oryziradicis sp. nov., respectively. The plant growth promoting effects of these strains suggest that they can be exploited to improve rice crop productivity. The type strain of D. rhizoryzae is LEGU1^T (KCTC 82712^T = NBRC 114485^T) and D. oryziradicis is G19^T (KCTC 82688^T = NBRC 114842^T).

A Pilot Study of Microbial Succession in Human Rib Skeletal Remains during Terrestrial Decomposition

The bones of decomposing vertebrates are colonized by a succession of diverse microbial communities. If this succession is similar across individuals, microbes may provide clues about the postmortem interval (PMI) during forensic investigations in which human skeletal remains are discovered. Here, we characterize the human bone microbial decomposer community to determine whether microbial succession is a marker for PMI. Six human donor subjects were placed outdoors to decompose on the soil surface at the Southeast Texas Applied Forensic Science facility. To also assess the effect of seasons, three decedents were placed each in the spring and summer. Once ribs were exposed through natural decomposition, a rib was collected from each body for eight time points at 3 weeks apart. We discovered a core bone decomposer microbiome dominated by taxa in the phylum Proteobacteria and evidence that these bone-invading microbes are likely sourced from the surrounding decomposition environment, including skin of the cadaver and soils. Additionally, we found significant overall differences in bone microbial community composition between seasons. Finally, we used the microbial community data to develop random forest models that predict PMI with an accuracy of approximately ±34 days over a 1- to 9-month time frame of decomposition. Typically, anthropologists provide PMI estimates based on qualitative information, giving PMI errors ranging from several months to years. Previous work has focused on only the characterization of the bone microbiome decomposer community, and this is the first known data-driven, quantitative PMI estimate of terrestrially decomposed human skeletal remains using microbial abundance information. IMPORTANCE Microbes are known to facilitate vertebrate decomposition, and they can do so in a repeatable, predictable manner. The succession of microbes in the skin and associated soil can be used to predict time since death during the first few weeks of decomposition. However, when remains are discovered after months or years, often the only evidence are skeletal remains. To determine if microbial succession in bone would be useful for estimating time since death after several months, human subjects were placed to decompose in the spring and summer seasons. Ribs were collected after 1 to 9 months of decomposition, and the bone microbial communities were characterized. Analysis revealed a core bone decomposer microbial community with some differences in microbial assembly occurring between seasons. These data provided time since death estimates of approximately ±34 days over 9 months. This may provide forensic investigators with a tool for estimating time since death of skeletal remains, for which there are few current methods.

Energetic Value of Elymus elongatus L. and Zea mays L. Grown on Soil Polluted with Ni2+, Co2+, Cd2+, and Sensitivity of Rhizospheric Bacteria to Heavy Metals

Plants, and microorganisms associated with them, offer an effective tool for removing pollutants, such as heavy metals, from the soil environment. The aim of this study was to determine changes caused by Ni2+, Co2+, and Cd2+ in the genetic diversity of soil-populating bacteria and the effect these heavy metals on the heating value of elongated coach grass (Elymus elongatus L.) and maize (Zea mays L.). Microorganisms support plants in removing heavy metals from soil. These plants can then be used for energetic purposes. The study aim was accomplished by determining counts of microorganisms and their resistance (RS) to Ni2+, Co2+, Cd2+, their colony development index (CD), ecophysiological diversity index (EP), and diversity established with the next generation sequencing (NGS) method. Further analyses aimed to establish test plants resistance to pollution with heavy metals and their heating value. Organotrophic bacteria turned out to be the most resistant to Co2+, whereas actinobacteria—to Cd2+ effects. At all taxonomic levels, the genetic diversity of bacteria was most adversely influenced by Cd2+ in the soil sown with Zea mays L. Bacteria belonging to Arthrobacter, Rhodoplanes, Kaistobacter, Devosia, Phycicoccus, and Thermomonas genera showed high tolerance to soil pollution with Ni2+, Co2+, and Cd2+, hence they should be perceived as potential sources of microorganisms useful for bioaugmentation of soils polluted with these heavy metals. Ni2+, Co2+, and Cd2+ had no effect on the heating value of Elymus elongatus L. and Zea mays L. The heating value of 1 kg of air-dry biomass of the tested plants was relatively high and ranged from 14.6 to 15.1 MJ. Elymus elongatus L. proved more useful in phytoremediation than Zea mays L.

Persistence and spread of tetracycline resistance genes and microbial community variations in the soil of animal corrals in a semi-arid planted forest

At the spring, goat and sheep herds are transferred to planted forests, in a semi-arid region in the northern Negev Desert, Israel, to reduce herbaceous biomass and, fire risk. The herds are held overnight in corrals for about 4 months, enriching the soil with organic matter and nitrogen. This research examined the effect of these enrichments on soil bacterial community structure (BCS) and the abundance of tetracycline resistance genes (TRGs) in active and abandoned corrals (1-10-years-old). Based on 16S rRNA gene sequences, the Proteobacteria and Actinobacteria phyla dominated the soil of all corrals. The Actinobacteria were less abundant in the active and 1-year-old corrals (23-26%) than in the other corrals and the control (33-38%). A principal component analysis showed that, the BCS in the active and the 1-year-old abandoned corrals was significantly different from that in the older corrals and the control. The Firmicutes phylum constituted 28% of the BCS in the active corrals, 12.5% in the 1-year-old corrals and 2% in the older corrals and the control. In contrast, the Acidobacteria phylum was hardly detected in the active and 1-year-old abandoned corrals and constituted 10% of the BCS in the older corrals. Genes conferring resistance to tetracycline were detected in high numbers. The tetG and tetW genes were detected in the active and abandoned corrals (1-10 years). The tetQ gene was detected only in the active and 1-year-old abandoned corrals. None of the genes were detected in the control soil. The three genes were detected outside an active corral, in the downstream section of an ephemeral tributary. The results prove that abandoned and unobserved periodic animal corrals are an environmental reservoir for TRGs.

Post-reclamation microbial diversity and functions in hexachlorocyclohexane (HCH) contaminated soil in relation to spontaneous HCH tolerant vegetation

The toxicity, volatility and persistence of the obsolete organochlorine pesticide hexachlorocyclohexane (HCH), makes reclamation of contaminated areas a priority for the health and welfare of neighboring human communities. Microbial diversity and functions and their relation to spontaneous vegetation in post-excavation situations, are essential indicators to consider in bioaugmentation or microbe-assisted phytoremediation strategies at field scale. Our study aimed to evaluate the effects of long-term HCH contamination on soil and plant-associated microbial communities, and whether contaminated soil has the potential to act as a bacterial inoculum in post-excavation bioremediation strategies. To scrutinize the role of vegetation, the potential nitrogen fixation of free-living and symbiotic diazotrophs of the legume Lotus tenuis was assessed as a measure of nutrient cycling functions in soil under HCH contamination. Potential nitrogen fixation was generally not affected by HCH, with the exception of lower nifH gene counts in excavated contaminated rhizospheres, most probably a short-term HCH effect on early bacterial succession in this compartment. HCH shaped microbial communities in long-term contaminated bulk soil, where we identified possible HCH tolerants such as Sphingomonas and Altererythrobacter. In L. tenuis rhizosphere, microbial community composition was additionally influenced by plant growth stage. Sphingobium and Massilia were the bacterial genera characteristic for HCH contaminated rhizospheres. Long-term HCH contamination negatively affected L. tenuis growth and development. However, root-associated bacterial community composition was driven solely by plant age, with negligible HCH effect. Results showed that L. tenuis acquired possible HCH tolerant bacteria such as the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade, Sphingomonas, Massilia or Pantoea which could simultaneously offer plant growth promoting (PGP) benefits for the host. Finally, we identified an inoculum with possibly HCH tolerant, PGP bacteria transferred from the contaminated bulk soil to L. tenuis roots through the rhizosphere compartment, consisting of Mesorhizobium loti, Neorhizobium galegae, Novosphingobium lindaniclasticum, Pantoea agglomerans and Lysobacter bugurensis.

A pilot study characterizing gravesoil bacterial communities a decade after swine decomposition

Vertebrate decomposition leads to an efflux of fluids rich with biochemicals and microbes from the carcass into the surrounding soil affecting the endogenous soil bacterial community. These perturbations are detectable in soils associated with carcasses (gravesoil) and influence soil bacterial ecology for years after the decomposition event, but it is unknown for how long. Measuring these impacts over extended timescales is critical to expanding vertebrate decomposition's role in the ecosystem and may provide useful information to forensic science. Using 16S rRNA gene amplicon data, this study surveyed bacterial composition in terrestrial soils associated with surface-exposed swine decomposition for 10 years after carcass placement. This pilot study utilizes the increased statistical power associated with repeated measure/within-subjects sampling to analyze bacterial diversity trends over time. Our results demonstrate that the soil bacterial diversity was significantly impacted by decomposition, with this impact being localized to the area underneath the carcass. Bacterial community dissimilarity was greatest 12 months postmortem before beginning recovery. Additionally, random forest regressions were utilized to determine 10 important genera for distinguishing decomposition timepoints, an important component of forensic investigations. Of these 10 genera, four were further analyzed for their significant relative abundance shifts underneath the carcass. This pilot study helps expand the current knowledge of long-term effects of carcass decomposition on soil bacterial communities, and is the first to our knowledge to characterize these communities temporally from placement through a decade of decomposition.

Phylogenomic Framework for Taxonomic Delineation of Paracoccus spp. and Exploration of Core-Pan Genome

The taxonomic classification of metabolically versatile Paracoccus spp. has been so far performed using polyphasic approach. The topology of single gene phylogenies, however, has highlighted ambiguous species assignments. In the present study, genome based multi-gene phylogenies and overall genome related index were used for species threshold assessment. Comprehensive phylogenomic analysis of Paracoccus genomes (n = 103) showed concordant clustering of strains across multi-gene marker set phylogenies (nMC = 0.08-0.14); as compared to 16S rDNA phylogeny (nMC = 0.37-0.42) suggesting robustness of multi gene phylogenies in drawing phylogenetic inferences. Functional gene content distribution across the genus showed that only 1.7% gene content constitutes the core genome highlighting the significance of extensive genomic variability in the evolution of Paracoccus spp. Further, genome metrics were used to validate characterized strains, identifying classification anomalies (n = 13), and based on this, genome derived taxonomic amendments were notified in present study. Conclusively, validated metric tools can be employed on whole genome sequences, including draft assemblies, for the assessment and assignment of uncharacterized strains and species level ascription of newly isolated Paracoccus strains in future.

Bioaugmentation potential evaluation of a bacterial consortium composed of isolated Pseudomonas and Rhodococcus for degrading benzene, toluene and styrene in sludge and sewage

Bioaugmentation was conducted using a bacterial consortium of Pseudomonas putida SW-3 and Rhodococcus ruber SS-4, to test their ability to degrade benzene, toluene, and styrene (BTS). SW-3 and SS-4 were isolated from domestic sludge and sewage samples to establish a synthetic consortium with an optimized ratio of 2:1 to reach a degradation efficiency of 82.5-89.8% of BTS. The bacterial consortium was inoculated with sludge and sewage samples at a ratio of 2:1, resulting in a degradation efficiency of 97.9% and 92.7%, respectively, at a BTS concentration of 1800 mg·L^-1. Analysis of bacterial community structure following bioaugmentation indicated an increase in abundance of BTS-degrading bacteria, particularly Acinetobacter and Pseudoxanthomonas in sludge and Pseudomonas in sewage, enhancing the collective BTS degradation ability of the bacterial community. Principal component analysis demonstrated that a more balanced bacterial community structure was established following intervention. This indicated that the selected bacteria are excellent candidates for bioaugmentation.

Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae

The genus Parapedobacter was established to describe a novel genus within the family Sphingobacteriaceae and derives its name from Pedobacter, with which it is shown to be evolutionarily related. Despite this, Parapedobacter and Pedobacter do not share very high 16S rRNA gene sequence similarities. Therefore, we hypothesized whether these substantial differences at the 16S rRNA gene level depict the true phylogeny or that these genomes have actually diverged. Thus, we performed genomic analysis of the four available genomes of Parapedobacter to better understand their phylogenomic position within family Sphingobacteriaceae. Our results demonstrated that Parapedobacter is more closely related to species of Olivibacter, as opposed to the genus Pedobacter. Further, we identified a significant class of enzymes called pectinases with potential industrial applications within the genomes of Parapedobacter luteus DSM 22899^T and Parapedobacter composti DSM 22900^T. These enzymes, specifically pectinesterases and pectate lyases, are presumed to have largely different catalytic activities based on very low sequence similarities to already known enzymes and thus may be exploited for industrial applications. We also determined the complete Bacteroides aerotolerance (Bat) operon (batA, batB, batC, batD, batE, hypothetical protein, moxR, and pa3071) within the genome of Parapedobacter indicus RK1^T. This expands the definition of genus Parapedobacter to containing members that are able to tolerate oxygen stress using encoded oxidative stress responsive systems. By conducting a signal propagation network analysis, we determined that BatD, BatE, and hypothetical proteins are the major controlling hubs that drive the expression of Bat operon. As a key metabolic difference, we also annotated the complete iol operon within the P. indicus RK1^T genome for utilization of all three stereoisomers of inositol, namely myo-inositol, scyllo-inositol, and 1D-chiro-inositol, which are abundant sources of organic phosphate found in soils. The results suggest that the genus Parapedobacter holds promising applications owing to its environmentally relevant genomic adaptations, which may be exploited in the future.

Bacterial Microbiota Isolated from Cysts of Globodera rostochiensis (Nematoda: Heteroderidae)

The potato cyst nematode (PCN) Globodera rostochiensis is a plant parasite of potato classified into a group of quarantine organisms causing high economic losses worldwide. Due to the long persistence of the parasite in soil, cysts harbor numerous bacteria whose presence can lead to cyst death and population decline. The cysts of G. rostochiensis found in two potato fields were used as a source of bacteria. The universal procedure was applied to extract DNA from bacteria which was then sequenced with 16S primers. The aims of the study were to identify bacterial microbiota associated with the PCN populations and to infer their phylogenetic relationships based on the maximum likelihood and Bayesian phylogeny of the 16S sequences. In addition, the impact of the most significant climate and edaphic factors on bacterial diversity were evaluated. Regarding the higher taxonomy, our results indicate that the prevalent bacterial classes were Bacilli, Actinobacteria and Alphaproteobacteria. Phylogenetic analyses clustered Brevibacterium frigoritolerans within the family Bacillaceae, confirming its recent reclassification. Long-term climate factors, such as air temperature, insolation hours, humidity and precipitation, as well as the content of soil organic matter, affected the bacterial diversity. The ability of cyst nematodes to persist in soil for a long time qualifies them as a significant natural source to explore the soil bacterial microbiota.