Taxonomic Diversity and Functional Traits of Soil Bacterial Communities under Radioactive Contamination: A Review

Studies investigating the taxonomic diversity and structure of soil bacteria in areas with enhanced radioactive backgrounds have been ongoing for three decades. An analysis of data published from 1996 to 2024 reveals changes in the taxonomic structure of radioactively contaminated soils compared to the reference, showing that these changes are not exclusively dependent on contamination rates or pollutant compositions. High levels of radioactive exposure from external irradiation and a high radionuclide content lead to a decrease in the alpha diversity of soil bacterial communities, both in laboratory settings and environmental conditions. The effects of low or moderate exposure are not consistently pronounced or unidirectional. Functional differences among taxonomic groups that dominate in contaminated soil indicate a variety of adaptation strategies. Bacteria identified as multiple-stress tolerant; exhibiting tolerance to metals and antibiotics; producing antioxidant enzymes, low-molecular antioxidants, and radioprotectors; participating in redox reactions; and possessing thermophilic characteristics play a significant role. Changes in the taxonomic and functional structure, resulting from increased soil radionuclide content, are influenced by the combined effects of ionizing radiation, the chemical toxicity of radionuclides and co-contaminants, as well as the physical and chemical properties of the soil and the initial bacterial community composition. Currently, the quantification of the differential contributions of these factors based on the existing published studies presents a challenge.

Conditioner application improves bedding quality and bacterial composition with potential beneficial impacts for dairy cow's health

Recycled manure solids (RMS) is used as bedding material in cow housing but can be at risk for pathogens development. Cows spend several hours per day lying down, contributing to the transfer of potential mastitis pathogens from the bedding to the udder. The effect of a bacterial conditioner (Manure Pro, MP) application was studied on RMS-bedding and milk qualities and on animal health. MP product was applied on bedding once a week for 3 months. Bedding and teat skin samples were collected from Control and MP groups at D01, D51, and D90 and analyzed through 16S rRNA amplicon sequencing. MP application modified bacterial profiles and diversity. Control bedding was significantly associated with potential mastitis pathogens, while no taxa of potential health risk were significantly detected in MP beddings. Functional prediction identified enrichment of metabolic pathways of agronomic interest in MP beddings. Significant associations with potential mastitis pathogens were mainly observed in Control teat skin samples. Finally, significantly better hygiene and lower Somatic Cell Counts in milk were observed for cows from MP group, while no group impact was observed on milk quality and microbiota. No dissemination of MP strains was observed from bedding to teats or milk.

IMPORTANCE

The use of Manure Pro (MP) conditioner improved recycled manure solids-bedding quality and this higher sanitary condition had further impacts on dairy cows' health with less potential mastitis pathogens significantly associated with bedding and teat skin samples of animals from MP group. The animals also presented an improved inflammation status, while milk quality was not modified. The use of MP conditioner on bedding may be of interest in controlling the risk of mastitis onset for dairy cows and further associated costs.

Colony-Based Electrochemistry Reveals Electron Conduction Mechanisms Mediated by Cytochromes and Flavins in Shewanella oneidensis

Bacteria utilize electron conduction in their communities to drive their metabolism, which has led to the development of various environmental technologies, such as electrochemical microbial systems and anaerobic digestion. It is challenging to measure the conductivity among bacterial cells when they hardly form stable biofilms on electrodes. This makes it difficult to identify the biomolecules involved in electron conduction. In the present study, we aimed to identify c-type cytochromes involved in electron conduction in Shewanella oneidensis MR-1 and examine the molecular mechanisms. We established a colony-based bioelectronic system that quantifies bacterial electrical conductivity, without the need for biofilm formation on electrodes. This system enabled the quantification of the conductivity of gene deletion mutants that scarcely form biofilms on electrodes, demonstrating that c-type cytochromes, MtrC and OmcA, are involved in electron conduction. Furthermore, the use of colonies of gene deletion mutants demonstrated that flavins participate in electron conduction by binding to OmcA, providing insight into the electron conduction pathways at the molecular level. Furthermore, phenazine-based electron transfer in Pseudomonas aeruginosa PAO1 and flavin-based electron transfer in Bacillus subtilis 3610 were confirmed, indicating that this colony-based system can be used for various bacteria, including weak electricigens.

Phyllosphere bacterial community dynamics in response to bacterial wildfire disease: succession and interaction patterns

Plants interact with complex microbial communities in which microorganisms play different roles in plant development and health. While certain microorganisms may cause disease, others promote nutrient uptake and resistance to stresses through a variety of mechanisms. Developing plant protection measures requires a deeper comprehension of the factors that influence multitrophic interactions and the organization of phyllospheric communities. High-throughput sequencing was used in this work to investigate the effects of climate variables and bacterial wildfire disease on the bacterial community's composition and assembly in the phyllosphere of tobacco (Nicotiana tabacum L.). The samples from June (M1), July (M2), August (M3), and September (M4) formed statistically separate clusters. The assembly of the whole bacterial population was mostly influenced by stochastic processes. PICRUSt2 predictions revealed genes enriched in the M3, a period when the plant wildfire disease index reached climax, were associated with the development of the wildfire disease (secretion of virulence factor), the enhanced metabolic capacity and environmental adaption. The M3 and M4 microbial communities have more intricate molecular ecological networks (MENs), bursting with interconnections within a densely networked bacterial population. The relative abundances of plant-beneficial and antagonistic microbes Clostridiales, Bacillales, Lactobacillales, and Sphingobacteriales, showed significant decrease in severally diseased sample (M3) compared to the pre-diseased samples (M1/M2). Following the results of MENs, we further test if the correlating bacterial pairs within the MEN have the possibility to share functional genes and we have unraveled 139 entries of such horizontal gene transfer (HGT) events, highlighting the significance of HGT in shaping the adaptive traits of plant-associated bacteria across the MENs, particularly in relation to host colonization and pathogenicity.

Bacterial community assessment of drinking water and downstream distribution systems in highland localities of Ecuador

Bacterial communities in drinking water provide a gauge to measure quality and confer insights into public health. In contrast to urban systems, water treatment in rural areas is not adequately monitored and could become a health risk. We performed 16S rRNA amplicon sequencing to analyze the microbiome present in the water treatment plants at two rural communities, one city, and the downstream water for human consumption in schools and reservoirs in the Andean highlands of Ecuador. We tested the effect of water treatment on the diversity and composition of bacterial communities. A set of physicochemical variables in the sampled water was evaluated and correlated with the structure of the observed bacterial communities. Predominant bacteria in the analyzed communities belonged to Proteobacteria and Actinobacteria. The Sphingobium genus, a chlorine resistance group, was particularly abundant. Of health concern in drinking water reservoirs were Fusobacteriaceae, Lachnospiraceae, and Ruminococcaceae; these families are associated with human and poultry fecal contamination. We propose the latter families as relevant biomarkers for establishing local standards for the monitoring of potable water systems in highlands of Ecuador. Our assessment of bacterial community composition in water systems in the Ecuadorian highlands provides a technical background to inform management decisions.

Developmental Shifts in the Microbiome of a Cosmopolitan Pest: Unraveling the Role of Wolbachia and Dominant Bacteria

Wolbachia bacteria (phylum Proteobacteria) are ubiquitous intracellular parasites of diverse invertebrates. In insects, coevolution has forged mutualistic associations with Wolbachia species, influencing reproduction, immunity, development, pathogen resistance, and overall fitness. However, the impact of Wolbachia on other microbial associates within the insect microbiome, which are crucial for host fitness, remains less explored. The diamondback moth (Plutella xylostella), a major pest of cruciferous vegetables worldwide, harbors the dominant Wolbachia strain plutWB1, known to distort its sex ratio. This study investigated the bacterial community diversity and dynamics across different developmental life stages and Wolbachia infection states in P. xylostella using high-throughput 16S rDNA amplicon sequencing. Proteobacteria and Firmicutes dominated the P. xylostella microbiome regardless of life stage or Wolbachia infection. However, the relative abundance of dominant genera, including an unclassified genus of Enterobacteriaceae, Wolbachia, Carnobacterium, and Delftia tsuruhatensis, displayed significant stage-specific variations. While significant differences in bacterial diversity and composition were observed across life stages, Wolbachia infection had no substantial impact on overall diversity. Nonetheless, relative abundances of specific genera differed between infection states. Notably, Wolbachia exhibited a stable, high relative abundance across all stages and negatively correlated with an unclassified genus of Enterobacteriaceae, Delftia tsuruhatensis, and Carnobacterium. Our findings provide a foundational understanding of the complex interplay between the host, Wolbachia, and the associated microbiome in P. xylostella, paving the way for a deeper understanding of their complex interactions and potential implications for pest control strategies.

Habitat-specific patterns of bacterial communities in a glacier-fed lake on the Tibetan Plateau

Different types of inlet water are expected to affect microbial communities of lake ecosystems due to changing environmental conditions and the dispersal of species. However, knowledge of the effects of changes in environmental conditions and export of microbial assemblages on lake ecosystems is limited, especially for glacier-fed lakes. Here, we collected water samples from the surface water of a glacier-fed lake and its two fed streams on the Tibetan Plateau to investigate the importance of glacial and non-glacial streams as sources of diversity for lake bacterial communities. Results showed that the glacial stream was an important source of microorganisms in the studied lake, contributing 45.53% to the total bacterial community in the lake water, while only 19.14% of bacterial community in the lake water was seeded by the non-glacial stream. Bacterial communities were significantly different between the glacier-fed lake and its two fed streams. pH, conductivity, total dissolved solids, water temperature and total nitrogen had a significant effect on bacterial spatial turnover, and together explained 36.2% of the variation of bacterial distribution among habitats. Moreover, bacterial co-occurrence associations tended to be stronger in the lake water than in stream habitats. Collectively, this study may provide an important reference for assessing the contributions of different inlet water sources to glacier-fed lakes.

The Great Gobi A Strictly Protected Area: Characterization of Soil Bacterial Communities from Four Oases

Understanding how microbial communities survive in extreme environmental pressure is critical for interpreting ecological patterns and microbial diversity. Great Gobi A Strictly Protected Area represents an intriguing model for studying the bacterial community since it is a protected and intact wild area of the Mongolian desert. In this work, the composition of a bacterial community of the soil from four oases was characterized by extracting total DNA and sequencing through the Illumina NovaSeq platform. In addition, the soil's chemical and physical properties were determined, and their influence on shaping the microbial communities was evaluated. The results showed a high variability of bacterial composition among oases. Moreover, combining specific chemical and physical parameters significantly shapes the bacterial community among oases. Data obtained suggested that the oases were highly variable in physiochemical parameters and bacterial communities despite the similar extreme climate conditions. Moreover, core functional microbiome were constituted by aerobic chemoheterotrophy and chemoheterotrophy, mainly contributed by the most abundant bacteria, such as Actinobacteriota, Pseudomonadota, and Firmicutes. This result supposes a metabolic flexibility for sustaining life in deserts. Furthermore, as the inhabitants of the extreme regions are likely to produce new chemical compounds, isolation of key taxa is thus encouraged.

Root-associated bacterial communities and root metabolite composition are linked to nitrogen use efficiency in sorghum

The development of cereal crops with high nitrogen use efficiency (NUE) is a priority for worldwide agriculture. In addition to conventional plant breeding and genetic engineering, the use of the plant microbiome offers another approach to improving crop NUE. To gain insight into the bacterial communities associated with sorghum lines that differ in NUE, a field experiment was designed comparing 24 diverse Sorghum bicolor lines under sufficient and deficient nitrogen (N). Amplicon sequencing and untargeted gas chromatography-mass spectrometry were used to characterize the bacterial communities and the root metabolome associated with sorghum genotypes varying in sensitivity to low N. We demonstrated that N stress and sorghum type (energy, sweet, and grain sorghum) significantly impacted the root-associated bacterial communities and root metabolite composition of sorghum. We found a positive correlation between sorghum NUE and bacterial richness and diversity in the rhizosphere. The greater alpha diversity in high NUE lines was associated with the decreased abundance of a dominant bacterial taxon, Pseudomonas. Multiple strong correlations were detected between root metabolites and rhizosphere bacterial communities in response to low N stress. This indicates that the shift in the sorghum microbiome due to low N is associated with the root metabolites of the host plant. Taken together, our findings suggest that host genetic regulation of root metabolites plays a role in defining the root-associated microbiome of sorghum genotypes differing in NUE and tolerance to low N stress.IMPORTANCEThe development of crops that are more nitrogen use-efficient (NUE) is critical for the future of the enhanced sustainability of agriculture worldwide. This objective has been pursued mainly through plant breeding and plant molecular engineering, but these approaches have had only limited success. Therefore, a different strategy that leverages soil microbes needs to be fully explored because it is known that soil microbes improve plant growth through multiple mechanisms. To design approaches that use the soil microbiome to increase NUE, it will first be essential to understand the relationship among soil microbes, root metabolites, and crop productivity. Using this approach, we demonstrated that certain key metabolites and specific microbes are associated with high and low sorghum NUE in a field study. This important information provides a new path forward for developing crop genotypes that have increased NUE through the positive contribution of soil microbes.

Simultaneous Two- and Three-Photon Deep Imaging of Autofluorescence in Bacterial Communities

The intrinsic fluorescence of bacterial samples has a proven potential for label-free bacterial characterization, monitoring bacterial metabolic functions, and as a mechanism for tracking the transport of relevant components through vesicles. The reduced scattering and axial confinement of the excitation offered by multiphoton imaging can be used to overcome some of the limitations of single-photon excitation (e.g., scattering and out-of-plane photobleaching) to the imaging of bacterial communities. In this work, we demonstrate in vivo multi-photon microscopy imaging of Streptomyces bacterial communities, based on the excitation of blue endogenous fluorophores, using an ultrafast Yb-fiber laser amplifier. Its parameters, such as the pulse energy, duration, wavelength, and repetition rate, enable in vivo multicolor imaging with a single source through the simultaneous two- and three-photon excitation of different fluorophores. Three-photon excitation at 1040 nm allows fluorophores with blue and green emission spectra to be addressed (and their corresponding ultraviolet and blue single-photon excitation wavelengths, respectively), and two-photon excitation at the same wavelength allows fluorophores with yellow, orange, or red emission spectra to be addressed (and their corresponding green, yellow, and orange single-photon excitation wavelengths). We demonstrate that three-photon excitation allows imaging over a depth range of more than 6 effective attenuation lengths to take place, corresponding to an 800 micrometer depth of imaging, in samples with a high density of fluorescent structures.

Microalgae Inoculation Significantly Shapes the Structure, Alters the Assembly Process, and Enhances the Stability of Bacterial Communities in Shrimp-Rearing Water

Intensive shrimp farming may lead to adverse environmental consequences due to discharged water effluent. Inoculation of microalgae can moderate the adverse effect of shrimp-farming water. However, how bacterial communities with different lifestyles (free-living (FL) and particle-attached (PA)) respond to microalgal inoculation is unclear. In the present study, we investigated the effects of two microalgae (Nannochloropsis oculata and Thalassiosira weissflogii) alone or in combination in regulating microbial communities in shrimp-farmed water and their potential applications. PERMANOVA revealed significant differences among treatments in terms of time and lifestyle. Community diversity analysis showed that PA bacteria responded more sensitively to different microalgal treatments than FL bacteria. Redundancy analysis (RDA) indicated that the bacterial community was majorly influenced by environmental factors, compared to microalgal direct influence. Moreover, the neutral model analysis and the average variation degree (AVD) index indicated that the addition of microalgae affected the bacterial community structure and stability during the stochastic process, and the PA bacterial community was the most stable with the addition of T. weissflogii. Therefore, the present study revealed the effects of microalgae and nutrient salts on bacterial communities in shrimp aquaculture water by adding microalgae to control the process of community change. This study is important for understanding the microbial community assembly and interpreting complex interactions among zoo-, phyto-, and bacterioplankton in shrimp aquaculture ecosystems. Additionally, these findings may contribute to the sustainable development of shrimp aquaculture and ecosystem conservation.

Evaluation of the Microbiome Identification of Forensically Relevant Biological Fluids: A Pilot Study

In forensic sciences, body fluids, or biological traces, are a major source of information, and their identification can play a decisive role in criminal investigations. Currently, the nature of biological fluids is assessed using immunological, physico-chemical, mRNA and epigenetic methods, but these have limits in terms of sensitivity and specificity. The emergence of next-generation sequencing technologies offers new opportunities to identify the nature of body fluids by determining bacterial communities. The aim of this pilot study was to assess whether analysis of the bacterial communities in isolated and mixed biological fluids could reflect the situation observed in real forensics labs. Several samples commonly encountered in forensic sciences were tested from healthy volunteers: saliva, vaginal fluid, blood, semen and skin swabs. These samples were analyzed alone or in combination in a ratio of 1:1. Sequencing was performed on the Ion Gene StudioTM S5 automated sequencer. Fluids tested alone revealed a typical bacterial signature with specific bacterial orders, enabling formal identification of the fluid of interest, despite inter-individual variations. However, in biological fluid mixtures, the predominance of some bacterial microbiomes inhibited interpretation. Oral and vaginal microbiomes were clearly preponderant, and the relative abundance of their bacterial communities and/or the presence of common species between samples made it impossible to detect bacterial orders or genera from other fluids, although they were distinguishable from one another. However, using the beta diversity, salivary fluids were identified and could be distinguished from fluids in combination. While this method of fluid identification is promising, further analyses are required to consolidate the protocol and ensure reliability.

Bacterial communities during composting cultivation of oyster mushroom Pleurotus floridanus using broken eggs as the nitrogen source and study of agronomic and nutritional properties

Introduction

Broken eggs are a byproduct of the poultry industry and a potential nitrogen source for mushroom cultivation. However, its feasibility needs to be evaluated experimentally.

Methods

In this study, a series of different addition amounts (0, 1.8, 3.6, 5.3 and 8.5%, w/w) of broken egg mixture (BEM) were applied in the composting cultivation process of oyster mushroom. The physicochemical properties and bacterial communities of composting substrate, and agronomic and nutritional properties of fruiting bodies were determined.

Results and discussion

The results showed that the BEM addition significantly (P < 0.05) increased the total nitrogen content in the composted substrate, and the contents of crude protein, total amino acids and essential amino acids of mushrooms. The P3 treatment (initial C/N of 26:1) showed the highest biological efficiency (BE) of 100.19% and a low contamination rate (CR) of 7.00%, while the higher dosage of BEM (P4 and P5) led to a sharp decrease in BE and a sharp increase in CR. High throughput sequencing revealed that the addition of BEM significantly (P < 0.05) changed the bacterial communities in the substrate at the beginning of composting. Streptococcus and Lactococcus were predominant bacterial genera in BEM treatments at the beginning stage of composting, while Acinetobacter became predominant at the ending stage. The co-occurrence network analysis showed that the P3 treatment demonstrated a much more complex bacterial community. The structural equation model analysis indicated that the addition of BEM affected the bacterial communities and nitrogen metabolism during composting, which further affected agronomic and nutritional properties of oyster mushrooms. An appropriate amount of BEM combined with composting processes can significantly improve the yield and quality of oyster mushroom, providing a new way for efficient utilization of BEM.

Does soil history decline in influencing the structure of bacterial communities of Brassica napus host plants across different growth stages?

Soil history has been shown to condition future rhizosphere microbial communities. However, previous experiments have also illustrated that mature, adult plants can "re-write," or mask, different soil histories through host plant-soil community feedbacks. This leaves a knowledge gap concerning how soil history influences bacterial community structure across different growth stages. Thus, here we tested the hypothesis that previously established soil histories will decrease in influencing the structure of Brassica napus bacterial communities over the growing season. We used an on-going agricultural field experiment to establish three different soil histories, plots of monocrop canola (B. napus), or rotations of wheat-canola, or pea-barley-canola. During the following season, we repeatedly sampled the surrounding bulk soil, rhizosphere, and roots of the B. napus hosts at different growth stages-the initial seeding conditions, seedling, rosette, bolting, and flower-from all three soil history plots. We compared composition and diversity of the B. napus soil bacterial communities, as estimated using 16S rRNA gene metabarcoding, to identify any changes associated with soil history and growth stages. We found that soil history remained significant across each growth stage in structuring the bacterial bulk soil and rhizosphere communities, but not the bacterial root communities. This suggests that the host plant's capacity to "re-write" different soil histories may be quite limited as key components that constitute the soil history's identity remain present, such that the previously established soil history continues to impact the bacterial rhizosphere communities, but not the root communities. For agriculture, this highlights how previously established soil histories persist and may have important long-term consequences on future plant-microbe communities, including bacteria.

Influences of Growth Stage and Ensiling Time on Fermentation Characteristics, Nitrite, and Bacterial Communities during Ensiling of Alfalfa

This study examined the impacts of growth stage and ensiling duration on the fermentation characteristics, nitrite content, and bacterial communities during the ensiling of alfalfa. Harvested alfalfa was divided into two groups: vegetative growth stage (VG) and late budding stage (LB). The fresh alfalfa underwent wilting until reaching approximately 65% moisture content, followed by natural fermentation. The experiment followed a completely randomized design, with samples collected after the wilting of alfalfa raw materials (MR) and on days 1, 3, 5, 7, 15, 30, and 60 of fermentation. The growth stage significantly influenced the chemical composition of alfalfa, with crude protein content being significantly higher in the vegetative growth stage alfalfa compared to that in the late budding stage (p < 0.05). Soluble carbohydrates, neutral detergent fiber, and acid detergent fiber content were significantly lower in the vegetative growth stage compared to the late budding stage (p < 0.05). Nitrite content, nitrate content, nitrite reductase activity, and nitrate reductase activity were all significantly higher in the vegetative growth stage compared to the late budding stage (p < 0.05). In terms of fermentation parameters, silage from the late budding stage exhibited superior characteristics compared to that from the vegetative growth stage. Compared to the alfalfa silage during the vegetative growth stage, the late budding stage group exhibited a higher lactate content and lower pH level. Notably, butyric acid was only detected in the silage from the vegetative growth stage group. Throughout the ensiling process, nitrite content, nitrate levels, nitrite reductase activity, and nitrate reductase activity decreased in both treatment groups. The dominant lactic acid bacteria differed between the two groups, with Enterococcus being predominant in vegetative growth stage alfalfa silage, and Weissella being predominant in late budding stage silage, transitioning to Lactiplantibacillus in the later stages of fermentation. On the 3rd day of silage fermentation, the vegetative growth stage group exhibited the highest abundance of Enterococcus, which subsequently decreased to its lowest level on the 15th day. Correlation analysis revealed that lactic acid bacteria, including Limosilactobacillus, Levilactobacillus, Loigolactobacillus, Pediococcus, Lactiplantibacillus, and Weissella, played a key role in nitrite and nitrate degradation in alfalfa silage. The presence of nitrite may be linked to Erwinia, unclassified_o__Enterobacterales, Pantoea, Exiguobacterium, Enterobacter, and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium.

Dietary of different forms of Humulus scandens on growth performance and intestinal bacterial communities in piglets

The present study was aimed at elucidating the effects of feeding different forms of Humulus scandens (Hu) on performance and bacterial communities in piglets. A total of 160 piglets were divided into four groups: (1) a control (CG, basal diet); (2) a basal diet with Hu pulp (HS), basal diet + Hu pulp; (3) a basal diet with Hu juice (HSJ), basal diet + Hu juice; and (4) a basal diet with Hu residue (HSR), basal diet + Hu residue. Results showed that HS, HSJ, and HSR supplementation led to rich average daily gain (ADG) and poor feed conversion ratio (FCR) during 28 to 70 d of age, increased 120 d body weight (BW), average daily feed intake (ADFI) and ADG and decreased FCR during 71 to 120 d of age. Three experiment groups presented greater (P < 0.05) IgA, IgG, and IgM and lower (P < 0.05) glucose, and blood urea nitrogen. The content of diamine oxidase significantly decreased (P < 0.05) in HS group. The crude  protein and crude fiber digestibility were improved (P < 0.05) in HS group and the Ca digestibility was increased (P < 0.05) in HS and HSJ groups. HSR supplementation improved the abundance of Firmicutes and decreased the abundance of Bacteroidetes. Hu supplementation with different forms increased the proportion of Lactobacillus in cecum content. These results indicated that supplemental feeding of Hu with different forms improved serum immunity, nutrient digestibility, and bacterial communities in piglets, promoting growth and development, which may be regarded as a reference for developing novel feed resources for piglets.

Freshwater Sponges as a Neglected Reservoir of Bacterial Biodiversity

Freshwater sponges (Spongillida: Demospongiae), including more than 240 described species, are globally distributed in continental waters (except for Antarctica), where they cover both natural and artificial surfaces. However, fragmentary studies have targeted their microbiome, making it difficult to test hypotheses about sponge-microbe specificity and metabolic relationships, along with the environmental factors playing key roles in structuring the associated microbial communities. To date, particular attention has been paid to sponges (family Lubomirskiidae) that are endemic to Lake Baikal. Few other freshwater sponge species (e.g., Ephydatia spp., Eunapius spp., and Spongilla lacustris), from lakes and rivers spanning from Europe to South and North America, have been targeted for microbiological studies. Representatives of the phyla Proteobacteria, Bacteroidetes, and Actinobacteria largely predominated, and high differences were reported between the microbiome of freshwater and marine sponges. Several bacterial strains isolated from freshwater sponges can produce bioactive compounds, mainly showing antibiotic activities, with potential application in biotechnology. Understanding the roles played by sponge microbiomes in freshwater ecosystems is still in its infancy and has yet to be clarified to disentangle the ecological and evolutionary significance of these largely under-investigated microbial communities. This review was aimed at providing the main available information on the composition and biotechnological potential of prokaryotic communities associated with healthy freshwater sponges, as a neglected component of the global sponge microbiome, to stimulate researchers interested in the field.

Differences in Bacterial Co-Occurrence Networks and Ecological Niches at the Surface Sediments and Bottom Seawater in the Haima Cold Seep

Cold seeps are highly productive chemosynthetic ecosystems in the deep-sea environment. Although microbial communities affected by methane seepage have been extensively studied in sediments and seawater, there is a lack of investigation of prokaryotic communities at the surface sediments and bottom seawater. We revealed the effect of methane seepage on co-occurrence networks and ecological niches of prokaryotic communities at the surface sediments and bottom seawater in the Haima cold seep. The results showed that methane seepage could cause the migration of Mn and Ba from the surface sediments to the overlying seawater, altering the elemental distribution at seepage sites (IS) compared with non-seepage sites (NS). Principal component analysis (PCA) showed that methane seepage led to closer distances of bacterial communities between surface sediments and bottom seawater. Co-occurrence networks indicated that methane seepage led to more complex interconnections at the surface sediments and bottom seawater. In summary, methane seepage caused bacterial communities in the surface sediments and bottom seawater to become more abundant and structurally complex. This study provides a comprehensive comparison of microbial profiles at the surface sediments and bottom seawater of cold seeps in the South China Sea (SCS), illustrating the impact of seepage on bacterial community dynamics.

Changes in the Bacterial Communities of Biocomposites with Different Flame Retardants

In today's world, the use of environmentally friendly materials is strongly encouraged. These materials derive from primary raw materials of plant origin, like fibrous hemp, flax, and bamboo, or recycled materials, such as textiles or residual paper, making them suitable for the growth of microorganisms. Here, we investigate changes in bacterial communities in biocomposites made of hemp shives, corn starch, and either expandable graphite or a Flovan compound as flame retardants. Using Next Generation Sequencing (NGS), we found that after 12 months of incubation at 22 °C with a relative humidity of 65%, Proteobacteria accounted for >99.7% of the microbiome in composites with either flame retardant. By contrast, in the absence of flame retardants, the abundance of Proteobacteria decreased to 32.1%, while Bacteroidetes (36.6%), Actinobacteria (8.4%), and Saccharobacteria (TM7, 14.51%) appeared. Using the increasing concentrations of either expandable graphite or a Flovan compound in an LB medium, we were able to achieve up to a 5-log reduction in the viability of Bacillus subtilis, Pseudomonas aeruginosa, representatives of the Bacillus and Pseudomonas genera, the abundance of which varied in the biocomposites tested. Our results demonstrate that flame retardants act on both Gram-positive and Gram-negative bacteria and suggest that their antimicrobial activities also have to be tested when producing new compounds.

α-Tomatine gradient across artificial roots recreates the recruitment of tomato root-associated Sphingobium

α-Tomatine is a major saponin that accumulates in tomatoes (Solanum lycopersicum). We previously reported that α-tomatine secreted from tomato roots modulates root-associated bacterial communities, particularly by enriching the abundance of Sphingobium belonging to the family Sphingomonadaceae. To further characterize the α-tomatine-mediated interactions between tomato plants and soil bacterial microbiota, we first cultivated tomato plants in pots containing different microbial inoculants originating from three field soils. Four bacterial genera, namely, Sphingobium, Bradyrhizobium, Cupriavidus, and Rhizobacter, were found to be commonly enriched in tomato root-associated bacterial communities. We constructed a pseudo-rhizosphere system using a mullite ceramic tube as an artificial root to investigate the influence of α-tomatine in modifying bacterial communities. The addition of α-tomatine from the artificial root resulted in the formation of a concentration gradient of α-tomatine that mimicked the tomato rhizosphere, and distinctive bacterial communities were observed in the soil close to the artificial root. Sphingobium was enriched according to the α-tomatine concentration gradient, whereas Bradyrhizobium, Cupriavidus, and Rhizobacter were not enriched in α-tomatine-treated soil. The tomato root-associated bacterial communities were similar to the soil bacterial communities in the vicinity of artificial root-secreting exudates; however, hierarchical cluster analysis revealed a distinction between root-associated and pseudo-rhizosphere bacterial communities. These results suggest that the pseudo-rhizosphere device at least partially creates a rhizosphere environment in which α-tomatine enhances the abundance of Sphingobium in the vicinity of the root. Enrichment of Sphingobium in the tomato rhizosphere was also apparent in publicly available microbiota data, further supporting the tight association between tomato roots and Sphingobium mediated by α-tomatine.

Salinity and host drive Ulva-associated bacterial communities across the Atlantic-Baltic Sea gradient

The green seaweed Ulva is a model system to study seaweed-bacteria interactions, but the impact of environmental drivers on the dynamics of these interactions is little understood. In this study, we investigated the stability and variability of the seaweed-associated bacteria across the Atlantic-Baltic Sea salinity gradient. We characterized the bacterial communities of 15 Ulva sensu lato species along 2,000 km of coastline in a total of 481 samples. Our results demonstrate that the Ulva-associated bacterial composition was strongly structured by both salinity and host species (together explaining between 34% and 91% of the variation in the abundance of the different bacterial genera). The largest shift in the bacterial consortia coincided with the horohalinicum (5-8 PSU, known as the transition zone from freshwater to marine conditions). Low-salinity communities especially contained high relative abundances of Luteolibacter, Cyanobium, Pirellula, Lacihabitans and an uncultured Spirosomaceae, whereas high-salinity communities were predominantly enriched in Litorimonas, Leucothrix, Sulfurovum, Algibacter and Dokdonia. We identified a small taxonomic core community (consisting of Paracoccus, Sulfitobacter and an uncultured Rhodobacteraceae), which together contributed to 14% of the reads per sample, on average. Additional core taxa followed a gradient model, as more core taxa were shared between neighbouring salinity ranges than between ranges at opposite ends of the Atlantic-Baltic Sea gradient. Our results contradict earlier statements that Ulva-associated bacterial communities are taxonomically highly variable across individuals and largely stochastically defined. Characteristic bacterial communities associated with distinct salinity regions may therefore facilitate the host's adaptation across the environmental gradient.

[Characteristics of Bacterial Community Structure in the Sediment of Rural Black and Odorous Water Bodies]

Sediment microorganisms are the main drivers of the material circulation and organic matter degradation processes in rural black and odorous water bodies(RBOWB), and the community structure of sediment microorganisms follows the changes in the external environment. Here, the pollutant indicators, including nitrogen, phosphorus, and heavy metals in the overlying water and sediment of 29 RBOWB in Dongming County of Heze City were measured, respectively. Combined with Illumina sequencing results, the composition and diversity characteristics of sediment bacterial communities in RBOWB and their correlation with environmental factors were further analyzed. The experimental results showed a wide distribution of pollutants in both of the overlying water and sediment in the RBOWB of this region. Compared with agricultural non-point source pollution, the concentrations of nitrogen and phosphorus pollutants in the overlying water with domestic sewage as the main source of pollution were 3.1 and 1.5 times higher than those of agricultural non-point source pollution, respectively. In addition, the contents of heavy metals in the sediments of RBOWB were generally lower than the soil element background value in Heze City. The dominant bacteria phyla in the sediments of the RBOWB were Proteobacteria, Actinobacteria, Chloroflexi, Firmicutes, and Acidobacteria, and the total abundance of these five dominant phyla accounted for 70.3%-83.6% of all sequences. The dominant classes were γ-Proteobacteria, α-Proteobacteria, Anaerolineae, and Actinobacteria. The dominant genera were Thiobacillus and Pseudarthrobacter. Moreover, Spearman correlation analysis showed that the environmental factors of DO, COD, TN, TP, and organic matter exerted significant effects(P<0.05) on sediment bacterial genera in RBOWB, and sediment bacterial community richness was significantly influenced by TN(P<0.05). The above results provided the microbiological knowledge for treating RBOWB.

Agronomic strategies to enhance the early vigor and yield of maize. Part I: the role of seed applied biostimulant, hybrid and starter fertilization on rhizosphere bacteria profile and diversity

The sustainable intensification of maize-based systems may reduce greenhouse-gas emissions and the excessive use of non-renewable inputs. Considering the key role that the microbiological fertility has on crop growth and resilience, it is worth of interest studying the role of cropping system on the rhizosphere bacterial communities, that affect soil health and biological soil fertility. In this work we monitored and characterized the diversity and composition of native rhizosphere bacterial communities during the early growth phases of two maize genotypes of different early vigor, using a nitrogen (N)-phosphorus (P) starter fertilization and a biostimulant seed treatment, in a growth chamber experiment, by polymerase chain reaction-denaturing gradient gel electrophoresis of partial 16S rRNA gene and amplicon sequencing. Cluster analyses showed that the biostimulant treatment affected the rhizosphere bacterial microbiota of the ordinary hybrid more than that of the early vigor, both at plant emergence and at the 5-leaf stage. Moreover, the diversity indices calculated from the community profiles, revealed significant effects of NP fertilization on richness and the estimated effective number of species (H2) in both maize genotypes, while the biostimulant had a positive effect on plant growth promoting community of the ordinary hybrid, both at the plant emergence and at the fifth leaf stage. Our data showed that maize genotype was the major factor shaping rhizosphere bacterial community composition suggesting that the root system of the two maize hybrids recruited a different microbiota. Moreover, for the first time, we identified at the species and genus level the predominant native bacteria associated with two maize hybrids differing for vigor. These results pave the way for further studies to be performed on the effects of cropping system and specific crop practices, considering also the application of biostimulants, on beneficial rhizosphere microorganisms.

Bacterial Microbiome Differences between the Roots of Diseased and Healthy Chinese Hickory (Carya cathayensis) Trees

Carya cathayensis is an important economic nut tree that is endemic to eastern China. As such, outbreaks of root rot disease in C. cathayensis result in reduced yields and serious economic losses. Moreover, while soil bacterial communities play a crucial role in plant health and are associated with plant disease outbreaks, their diversity and composition in C. cathayensis are not clearly understood. In this study, Proteobacteria, Acidobacteria, and Actinobacteria were found to be the most dominant bacterial communities (accounting for approximately 80.32% of the total) in the root tissue, rhizosphere soil, and bulk soil of healthy C. cathayensis specimens. Further analysis revealed the abundance of genera belonging to Proteobacteria, namely, Acidibacter, Bradyrhizobium, Paraburkholderia, Sphaerotilus, and Steroidobacter, was higher in the root tissues of healthy C. cathayensis specimens than in those of diseased and dead trees. In addition, the abundance of four genera belonging to Actinobacteria, namely, Actinoallomurus, Actinomadura, Actinocrinis, and Gaiella, was significantly higher in the root tissues of healthy C. cathayensis specimens than in those of diseased and dead trees. Altogether, these results suggest that disruption in the balance of these bacterial communities may be associated with the development of root rot in C. cathayensis, and further, our study provides theoretical guidance for the isolation and control of pathogens and diseases related to this important tree species.

Environmental Factors Affecting the Diversity and Composition of Environmental Microorganisms in the Shaoxing Rice Wine Producing Area

Shaoxing rice wine is a notable exemplar of Chinese rice wine. Its superior quality is strongly correlated with the indigenous natural environment. The results indicated that Firmicutes (75%), Actinobacteria (15%), Proteobacteria (5%), and Bacteroidetes (3%) comprised the prevailing bacterial groups. Among the main bacterial genera, Lactobacillus was the most abundant, accounting for 49.4%, followed by Lactococcus (11.9%), Saccharopolyspora (13.1%), Leuconostoc (4.1%), and Thermoactinomyces (1.1%). The dominant fungal phyla were Ascomycota and Zygomycota. Among the dominant genera, Saccharomyces (59.3%) prevailed as the most abundant, followed by Saccharomycopsis (10.7%), Aspergillus (7.1%), Thermomyces (6.2%), Rhizopus (4.9%), Rhizomucor (2.2%), and Mucor (1.3%). The findings demonstrate that the structure of the bacterial and fungal communities remains stable in the environment, with their diversity strongly influenced by climatic conditions. The continuous fluctuations in environmental factors, such as temperature, air pressure, humidity, rainfall, and light, significantly impact the composition and diversity of microbial populations, particularly the dominant bacterial community.

Canaries' Microbiota: The Gut Bacterial Communities along One Female Reproductive Cycle

Investigations of bacterial communities are on the rise both in human and veterinary medicine. Their role in health maintenance and pathogenic mechanisms is in the limelight of infectious, metabolic, and cancer research. Among the most considered, gut bacterial communities take the cake. Their part in animals was assessed mainly to improve animal production, public health, and pet management. In this regard, canaries deserve attention, being a popular pet and source of economic income for bird-keepers, for whom breeding represents a pivotal point. Thus, the present work aimed to follow gut bacterial communities' evolution along on whole reproductive cycle of 12 healthy female canaries. Feces were collected during parental care, molting, and resting phase, and submitted for 16S rRNA sequencing. Data were analyzed and a substantial presence of Lactobacillus aviarius along all the phases, and a relevant shift of microbiota during molting and rest due to an abrupt decrease of the Vermiphilaceae family were detected. Although the meaning of such change is not clear, future research may highlight unforeseen scenarios. Moreover, Lactobacillus aviarius may be deemed for normal bacteria flora restoration in debilitated birds, perhaps improving their health and productivity.

Metagenomic Insights into the Microbiome and Resistance Genes of Traditional Fermented Foods in Arabia

This study uncovered microbial communities and evaluated the microbiological safety of traditional fermented foods consumed in the Arab region. Samples of dairy and non-dairy fermented foods-mish, jibneh, zabadi, and pickles-were collected from local markets in Saudi Arabia. Using the MiSeq system, samples were sequenced using 16S amplicons and shotgun metagenomics. Alpha and beta diversity indicated inter- and intra-variation in the studied fermented foods' bacterial communities. In the case of mish, the replicates were clustered. Twenty-one genera were found to be significantly different (FDR < 0.05) in abundance in pairwise comparison of fermented foods. Five high-quality, metagenome-assembled genomes (MAGs) of Lactococcus lactis, Lactobacillus helveticus, Pseudoalteromonas nigrifaciens, Streptococcus thermophiles, and Lactobacillus acetotolerans were retrieved from the shotgun sequencing representing the dominant taxa in the studied fermented foods. Additionally, 33 genes that cause antimicrobial resistance (ARGs) against ten different antibiotic classes were detected. Metabolic pathways were abundant in the studied metagenomes, such as amino acid metabolism, carbohydrate metabolism, cofactors, and vitamin biosynthesis. Metagenomic evaluation of Arabian fermented foods, including the identification of probiotics, pathogenic bacteria, and ARGs, illustrates the importance of microbiological analysis in evaluating their health effects.

The Gill-Associated Bacterial Community Is More Affected by Exogenous Chlorella pyrenoidosa Addition than the Bacterial Communities of Water and Fish Gut in GIFT Tilapia (Oreochromis niloticus) Aquaculture System

Microalgae has been widely used in aquaculture to improve both the water environment and fish growth; however, the current understanding of the effects of microalgae addition on the key players involved in regulating the water environment and fish health, such as microorganisms, remains limited. Here, a 50-day mesocosm experiment was set up to simulate the culture of Genetic Improvement of Farmed Tilapia (GIFT, Oreochromis niloticus) with an average weight of 14.18 ± 0.93 g and an average length of 82.77 ± 2.80 mm. Different amounts of Chlorella pyrenoidosa were added into these artificial systems to investigate dynamics of bacterial communities in aquaculture water, fish gill, and gut using amplicon-based high-throughput sequencing technology. Our results showed that Chlorella pyrenoidosa addition increased diversity and network complexity of gill-associated bacterial communities rather than those of the water and gut. Furthermore, more biomarkers in the gill-associated bacterial communities were detected in response to Chlorella pyrenoidosa addition than the water and fish gut samples. These findings highlighted the high sensitivity of gill-associated bacterial communities in response to the Chlorella pyrenoidosa addition, implying Chlorella pyrenoidosa addition could play important roles in regulating the fish mucosal immunity by altering the gill-associated microbiota.

Dynamics of Bacterial Diversity and Functions with Physicochemical Properties in Different Phases of Pig Manure Composting

Bacteria are key drivers in regulating ecosystem functions, and understanding the diversity and dynamic changes in bacteria in composting is very important for optimizing compost. This study investigated the structure, composition, and function of bacterial communities in alkaline pig manure compost using Miseq sequencing, PICRUSt2. The ACE and Chao1 indices of the bacterial communities in various phases were significantly different. Bacterial communities of alkaline pig compost were different from neutral and acidic swine manure compost, and there were 438 genera of common bacteria in various stages. The main bacterium was the phylum Firmicutes. There were six genera, including Romboutsia, Clostridium, Terrisporobacter, norank_f_Marinococcaceae, Saccharomonospora, and unclassified_f_Bacillaceae, that were significantly correlated (p < 0.05), or even extremely significantly correlated (p < 0.001), with the physicochemical properties. TOC, moisture, C/N, and Tem were the key factors that caused changes in bacterial communities in composting. PICRUSt2 analysis showed that there were seven functional groups: metabolism (45.02-48.07%), environmental information processing (15.25-16.00%), genetic information processing (16.97-20.02%), cellular processes (3.63-4.37%), human diseases (0.71-0.82%), organismal systems (0.66-0.77%), and unclassified (13.93-14.36%). This study will provide a reference for improving bacteria growth and reproduction conditions in pig manure composting, optimizing the process, and improving the efficiency of composting.

Unraveling the roles of coastal bacterial consortia in degradation of various lignocellulosic substrates

Lignocellulose, as the most abundant natural organic carbon on earth, plays a key role in regulating the global carbon cycle, but there have been only few studies in marine ecosystems. Little information is available about the extant lignin-degrading bacteria in coastal wetlands, limiting our understanding of their ecological roles and traits in lignocellulose degradation. We utilized in situ lignocellulose enrichment experiments coupled with 16S rRNA amplicon and shotgun metagenomics sequencing to identify and characterize bacterial consortia attributed to different lignin/lignocellulosic substrates in the southern-east intertidal zone of East China Sea. We found the consortia enriched on woody lignocellulose showed higher diversity than those on herbaceous substrate. This also revealed substrate-dependent taxonomic groups. A time-dissimilarity pattern with increased alpha diversity over time was observed. Additionally, this study identified a comprehensive set of genes associated with lignin degradation potential, containing 23 gene families involved in lignin depolymerization, and 371 gene families involved in aerobic/anaerobic lignin-derived aromatic compound pathways, challenging the traditional view of lignin recalcitrance within marine ecosystems. In contrast to similar cellulase genes among the lignocellulose substrates, significantly different ligninolytic gene groups were observed between consortia under woody and herbaceous substrates. Importantly, we not only observed synergistic degradation of lignin and hemi-/cellulose, but also pinpointed the potential biological actors at the levels of taxa and functional genes, which indicated that the alternation of aerobic and anaerobic catabolism could facilitate lignocellulose degradation. Our study advances the understanding of coastal bacterial community assembly and metabolic potential for lignocellulose substrates. IMPORTANCE It is essential for the global carbon cycle that microorganisms drive lignocellulose transformation, due to its high abundance. Previous studies were primarily constrained to terrestrial ecosystems, with limited information about the role of microbes in marine ecosystems. Through in situ lignocellulose enrichment experiment coupled with high-throughput sequencing, this study demonstrated different impacts that substrates and exposure times had on long-term bacterial community assembly and pinpointed comprehensive, yet versatile, potential decomposers at the levels of taxa and functional genes in response to different lignocellulose substrates. Moreover, the links between ligninolytic functional traits and taxonomic groups of substrate-specific populations were revealed. It showed that the synergistic effect of lignin and hemi-/cellulose degradation could enhance lignocellulose degradation under alternation of aerobic and anaerobic conditions. This study provides valuable taxonomic and genomic insights into coastal bacterial consortia for lignocellulose degradation.

Profiles of bacterial communities and environmental factors associated with proliferation of malaria vector mosquitoes within the Kenyan Coast

Background

Since Anopheles mosquitoes which transmit and maintain the malaria parasite breed in the outdoor environment, there is an urgent need to manage these mosquito breeding sites. In order to elaborate more on the ecological landscape of mosquito breeding sites, the bacterial community structure and their interactions with physicochemical factors in mosquito larval habitats was characterised in Kwale County (Kenya), where malaria is endemic.

Methods

The physical characteristics and water physicochemical parameters of the habitats were determined and recorded. Water samples were also collected from the identified sites for total metagenomic DNA extraction in order to characterise the bacterial communities within the breeding sites.

Results and Discussion

Sites where mosquito larvae were found were described as positive and those without mosquito larvae as negative. Electrical conductivity, total dissolved solids, salinity and ammonia were lower in the rainy season than in the dry season, which also coincided with a high proportion of positive sites. Pseudomonadota was the most common phyla recovered in all samples followed by Bacteroidota and then Actinomycetota. The presence or absence of mosquito larvae in a potential proliferation site was not related to the bacterial community structure in the sampled sites, but was positively correlated with bacterial richness and evenness.

Conclusion

Generally, the presence of Anopheles mosquito larvae was found to be positively correlated with rainy season, bacterial richness and evenness, and negatively correlated with electrical conductivity, total dissolved solids, salinity and ammonia. The findings of this study have implications for predicting the potential of environmental water samples to become mosquito proliferation sites.

[Effects of Biochar Application on Physicochemical Properties and Bacterial Communities of Microplastic-contaminated Calcareous Soil]

Microplastics are widely distributed in the soil environment, threatening the soil ecological environment system and changing soil physicochemical properties and microbial characteristics. Biochar is often used as a soil amendment to improve soil quality due to its special pore structure and good soil nutrient retention ability. However, the understanding of the effects and mechanisms of biochar application on the physicochemical properties and bacterial communities of microplastic-contaminated soils is still very limited. Therefore, a 21-day micro-soil culture experiment was conducted to analyze the effects of biochar application on physicochemical properties and bacterial community changes in soil contaminated with different concentrations of microplastics using 16S rRNA high-throughput sequencing technology. The results revealed that the application of biochar slowed down the decrease in nitrate nitrogen and Olsen-P contents in microplastic-contaminated soil and increased the total phosphorus content. Biochar addition increased the relative abundance of tolerant phylum such as Acidobacteriota, Actinobacteriota, and Bacteroidota in microplastic-contaminated calcareous soil. Proteobacteria, Acidobacteriota, and Actinobacteriota were the dominant bacteria of the soil bacterial community in each treatment on day 7 and day 21. Compared with that on day 7, the relative abundance of Proteobacteria and Firmicutes significantly decreased, and the relative abundance of Acidobacteriota, Actinobacteriota, Bacteroidota, Chloroflexi, and Myxococcota increased on day 21. Biochar application also increased the relative abundance of Lysobacter in microplastic-contaminated soils. This study demonstrated that the application of biochar increased microplastic-resistant bacteria, enhanced the stability of microplastic-contaminated soil, and slowed down the pollution of microplastics to the soil. Moreover, biochar had great potential to improve the quality of microplastic-contaminated calcareous soil.

Indoor Bacterial and Fungal Burden in "Moldy" versus "Non-Moldy" Homes: A Case Study Employing Advanced Sequencing Techniques in a US Metropolitan Area

The presence of fungi in the indoor environment is associated with allergies and other respiratory symptoms. The aim of this study was to use sequencing and molecular methods, including next-generation sequencing (NGS) approaches, to explore the bacterial and fungal communities and their abundance in the indoor environment of houses (n = 20) with visible "moldy" (HVM) and nonvisible "non-moldy" (HNM) in Memphis, TN, USA. Dust samples were collected from air vents and ground surfaces, and the total DNA was analyzed for bacteria and fungi by amplifying 16S rRNA and ITS genes on the Illumina Miseq. Results indicated that Leptosphaerulina was the most abundant fungal genus present in the air vent and ground samples from HNM and HVM. At the same time, the most abundant bacterial genera in the air vent and ground samples were Propionibacterium and Streptococcus. The fungi community diversity was significantly different in the air vent samples. The abundance of fungal species known to be associated with respiratory diseases in indoor dust samples was similar, regardless of the visibility of fungi in the houses. The existence of fungi associated with respiratory symptoms was compared with several parameters like dust particulate matter (PM), CO2 level, temperature, and humidity. Most of these parameters are either positively or negatively correlated with the existence of fungi associated with respiratory diseases; however, none of these correlations were significant at p = 0.05. Our results indicate that implementing molecular methods for detecting indoor fungi may strengthen common exposure and risk assessment practices.

Infection density pattern of Cardinium affects the responses of bacterial communities in an invasive whitefly under heat conditions

Communities of bacteria, especially symbionts, are vital for the growth and development of insects and other arthropods, including Bemisia tabaci Mediterranean (MED), a destructive and invasive insect pest. However, the infection density patterns and influence factors of bacteria in whiteflies, which mainly include symbionts, remain largely unclear. To reveal the different density patterns of Cardinium in B. tabaci MED populations and the impacts of high temperatures on whiteflies with different Cardinium density infection patterns, 2 isofemale lines isolated from B. tabaci MED from the same geographical population of China and from B. tabaci MED collected from other countries and locations were examined using several techniques and methods, including fluorescence in situ hybridization (FISH), quantitative real-time polymerase chain reaction (qPCR), 16S rRNA gene sequencing, and 2b-RAD sequencing. The results showed that there were 2 different infection density patterns of Cardinium in B. tabaci MED (including 1 high-density pattern and 1 low-density pattern). For whiteflies with low-density Cardinium, conventional PCR could not detect Cardinium, but the other techniques confirmed that there was a low level of Cardinium within hosts. High temperature significantly decreased the diversity of bacterial communities: the relative titer of Cardinium increased but the density of Rickettsia decreased in the isofemale line with high-density Cardinium. However, high temperature did not influence the diversity and symbiont density in the line with low-density Cardinium. Moreover, high temperature influenced the functions of bacterial communities in whiteflies with high-density Cardinium but did not affect the bacterial functions in whiteflies with low-density Cardinium. Our results provide novel insights into the complex associations between symbionts and host insects.

Development of a Polymicrobial Checkerboard Assay as a Tool for Determining Combinatorial Antibiotic Effectiveness in Polymicrobial Communities

The checkerboard assay is a well-established tool used to determine the antimicrobial effects of two compounds in combination. Usually, data collected from the checkerboard assay use visible turbidity and optical density as a readout. While helpful in traditional checkerboard assays, these measurements become less useful in a polymicrobial context as they do not enable assessment of the drug effects on the individual members of the community. The methodology described herein allows for the determination of cell viability through selective and differential plating of each individual species in a community while retaining much of the high-throughput nature of a turbidity-based analysis and requiring no specialized equipment. This methodology further improves turbidity-based measurements by providing a distinction between bacteriostatic versus bactericidal concentrations of antibiotics. Herein, we use this method to demonstrate that the clinically used antibiotic combination of ceftazidime and gentamicin works synergistically against Pseudomonas aeruginosa in monoculture but antagonistically in a polymicrobial culture also containing Acinetobacter baumannii, Staphylococcus aureus, and Enterococcus faecalis, highlighting the fundamental importance of this methodology in improving clinical practices. We propose that this method could be implemented in clinical microbiology laboratories with minimal impact on the overall time for diagnosis.

[Effects of Biogas Slurry Application on Soil Microbial Communities Structure and Function During Wheat-rice Stubble Period]

To reveal the effects of biogas slurry application on soil microbial community structure and function, a soil column experiment was constructed with three treatments[(no N addition, CM; conventional fertilization, SN; biogas slurry addition, SZ)]. The differences in composition, diversity, and structure of bacterial and fungal communities on day 1 and day 21 after soil flooding were evaluated, and their functions were predicted using Illumina high-throughput sequencing technology. The results of the analysis of α diversity showed that the fungal α-diversity indexes of CM, SN, and SZ treatments on day 1 were significantly higher than those on day 21, and there was no significant difference among the three treatments. However, the bacterial Simpson index differed among the three treatments on day 21, with SZ-21 showing a higher Simpson index but lower Chao1 index compared with those of SZ-21. The analysis of bacterial community structure showed that Firmicutes, Chloroflexi, and Actinobacteria in the SN-1 treatment were different from those in the other treatments on day 1, whereas the relative abundance of bacterial phyla in the SZ and SN treatments were similar on day 21. The analysis of fungal community structure showed that the relative abundance of Ascomycota and Zygomycota in the SZ-1 treatment were higher than those in the SN-1 and CM-1 treatments on day 1. The relative abundance of Ascomycota in the SN-21 and SZ-21 treatments were lower, whereas that of Zygomycota were higher compared with that in CM-21. The analysis of NMDS showed that the composition of bacterial and fungal communities in the SN and SZ treatments showed a gradually similar trend. The PICRUSt analysis showed that the function of the soil bacterial community was similar in the CM, SN, and SZ treatments. The FUNGuild function prediction reflected that the main differences in trophic type between the SN-21 and SZ-21 treatments occurred in saprotroph and pathotroph forms. Therefore, biogas slurry addition in the wheat-rice stubble stage could contribute to balancing soil nutrients and maintaining soil ecological function to a certain extent, but there may still be a risk of fungal disease.

Bacterial Communities Vary from Different Scleractinian Coral Species and between Bleached and Non-Bleached Corals

Bleaching is one of the most relevant factors implicated in the integrity of coral reef ecosystems, with the increasing frequency and intensity of damaging events representing a serious threat to reef biodiversity. Here, we analyzed changes in coral-associated bacteria from three types of non-bleached and bleached scleractinian corals (Acropora digitifera, Galaxea fascicularis, and Porites pukoensis) in Hainan Luhuitou peninsula coastal areas. The community structure of symbiotic bacteria differed significantly among the three apparently healthy corals. The bleached corals had higher bacterial alpha diversity and some specific bacteria genera, including Ruegeria, Methyloceanibacter, Filomicrobium, Halioglobus, Rubripirellula, Rhodopirellula, Silicimonas, Blastopirellula, Sva0996 marine group, Woeseia, and unclassified_c_Gammaproteobacteria, were consistently increased in bleached groups. Network analysis revealed significantly different degrees of modularity between bleached and non-bleached groups at the bacterial genus level, and a higher proportion of links was dominated by positive co-occurrences. Functional prediction analysis illustrated that coral-associated bacteria remained relatively consistent in the bleached and non-bleached groups. Structure equation modeling revealed that the bacterial community diversity and function were directly influenced by host and environment factors. These findings suggested that coral-associated bacterial responses to bleaching occur in a host-dependent manner, informing novel strategies for restoring coral and aiding adaption to bleaching stress. IMPORTANCE Accumulating evidence indicates that coral-associated bacteria play an important role in the health of holobionts. However, the variability of the symbiotic bacterial community structure among coral species with different coral health statuses remains largely unknown. Here, we investigated three apparent non-bleached (healthy) and bleached coral species (sampled in situ), involving related symbiotic bacterial profiles, including composition, alpha diversity, network relationship, and potential function. Structural equation modeling analysis was used to analyze the relationship between coral status and abiotic and biotic factors. The bacterial community structure of different groups was shown to exhibit host-specific traits. Both host and environmental impacts had primary effects on coral-associated microbial communities. Future studies are needed to identify the mechanisms that mediate divergent microbial consortia.

Soil nutrients, enzyme activities, and bacterial communities in varied plant communities in karst rocky desertification regions in Wushan County, Southwest China

Vegetation restoration has become a common practice in karst rocky desertification (KRD) areas of southwestern China. The bacteria, which have made a connection between soil and plants, have been an important role in regulating the succession and restoration of karst vegetation. However, it is still unclear how soil bacterial communities and soil properties respond to natural vegetation restoration processes in karst areas. To address this gap, we investigated the soil nutrients, enzyme activity, and soil bacterial community among various plant communities, including farmland (FL), land with herbs only (SSI), herb-and-shrub land (SSII), woody thickets (SSIII), coniferous forest (SSIV), coniferous and broad-leaved mixed forest (SSV), and evergreen broad-leaved forest (SSVI). Our results found that SSII had the highest levels of soil organic matter, total nitrogen, available phosphorus, available nitrogen, sucrase, and β-glucosidase among all the plant communities. These results indicated that herb-and-shrub land have contributed to the rapid restoration of vegetation in KRD regions. FL exhibited the lowest levels of soil nutrients and enzyme activities, while showing the highest bacterial richness and diversity among all the plant communities. This suggested that appropriate human intervention can increase bacterial diversity and richness in the area. The predominant bacterial phylum also varied among the different plant communities, with Actinobacteria being the most abundant in SSI, SSII, SSIII, and SSIV, while Proteobacteria were the most abundant in SSV and SSVI. Furthermore, PCoA analysis demonstrated significant changes in the soil bacterial community structure, with SSI, SSII, SSIII, and SSIV had shared similar structures, while SSV and SSVI had comparable structures. As for soil characteristics, total phosphorus (TP) and total potassium (TK) were the primary factors affecting the soil bacterial community. SSV and SSVI had the most complex bacterial networks and were more stable than other groups. The genera Ktedonobacter, norank_f_Anaerolineaceae, and Vicinamibacter had the highest betweenness centrality scores and were identified as keystone genera in the co-occurrence network in KRD areas. In summary, our results have demonstrated that herb-and-shrub can promote community succession and increase soil nutrient levels in KRD regions.

Conserved organ-specific microbial assemblages in different populations of a terrestrial crab

Microorganisms are ubiquitous in the environment and provide genetic and physiological functions to multicellular organisms. Knowledge on the associated microbiota is becoming highly relevant to understand the host's ecology and biology. Among invertebrates, many examples of endosymbiosis have been described, such as those in corals, ants, and termites. At present, however, little is known on the presence, diversity, and putative roles of the microbiota associated to brachyuran crabs in relation to their environment. In this work we investigated the associated microbiota of three populations of the terrestrial brachyuran crab Chiromantes haematocheir to find evidence of a conserved organ-specific microbiome unrelated to the population of origin and dissimilar from environmental microbial assemblages. Bacterial 16S rRNA gene and fungal ITS sequences were obtained from selected crab organs and environmental matrices to profile microbial communities. Despite the presence of truly marine larval stages and the absence of a gregarious behaviour, favouring microbiota exchanges, we found common, organ-specific microbiota, associated with the gut and the gills of crabs from the different populations (with more than 15% of the genera detected specifically enriched only in one organ). These findings suggest the presence of possible functional roles of the organ-specific microbiota.

Effect of Snowmelt on Groundwater Bacterial Community Composition and Potential Role of Surface Environments as Microbial Seed Bank in Two Distinct Aquifers from the Region of Quebec, Canada

Events of groundwater recharge are associated with changes in the composition of aquifer microbial communities but also abiotic conditions. Modification in the structure of the community can be the result of different environmental condition favoring or hindering certain taxa, or due to the introduction of surface-derived taxa. Yet, in both cases, the local hydrogeochemical settings of the aquifer is likely to affect the amount of variation observed. Therefore, in our study, we used 16S rRNA gene sequencing to assess how microbial communities change in response to snowmelt and the potential connectivity between subsurface and surface microbiomes in two distinct aquifers located in the region of Vaudreuil-Soulanges (Québec, Canada). At both sites, we observed an increase in groundwater level and decrease in temperature following the onset of snow melt in March 2019. Bacterial community composition of each aquifer was significantly different (p < 0.05) between samples collected prior and after groundwater recharge. Furthermore, microbial source tracking results suggested a low contribution of surface environments to the groundwater microbiome except for in the months associated with recharge (March 2019 and April 2019). Overall, despite differences in soil permeability between both sites, the period of snow melt was followed by important changes in the composition of microbial communities from aquifers.

Spatial patterns in host-associated and free-living bacterial communities across six temperate estuaries

A major goal of microbial ecology is to establish the importance of spatial and environmental factors in driving community variation. Their relative importance likely varies across spatial scales, but focus has primarily been on free-living communities within well-connected aquatic environments rather than less connected island-like habitats such as estuaries, and key host-associated communities within these systems. Here we sampled both free-living (seawater and sediment) and host-associated (estuarine fish hindgut microbiome, Pelates sexlineatus) communities across six temperate Australian estuaries spanning ∼500 km. We find that spatial and environmental factors have different influences on these communities, with seawater demonstrating strong distance-decay relationships (R = -0.69) and significant associations with a range of environmental variables. Distance-decay relationships were weak for sediment communities but became stronger over smaller spatial scales (within estuaries, R = -0.5) potentially reflecting environmental filtering across biogeochemical gradients or stochastic processes within estuary sediments. Finally, P. sexlineatus hindgut microbiome communities displayed weak distance-decay relationships (R = -0.36) and limited variation explained by environmental variables, indicating the significance of host-related factors in driving community variation. Our findings provide important ecological insights into the spatial distributions and driving forces of both free-living and host-associated bacterial patterns across temperate estuarine systems.

Quantification of metabolic niche occupancy dynamics in a Baltic Sea bacterial community

Progress in molecular methods has enabled the monitoring of bacterial populations in time. Nevertheless, understanding community dynamics and its links with ecosystem functioning remains challenging due to the tremendous diversity of microorganisms. Conceptual frameworks that make sense of time-series of taxonomically-rich bacterial communities, regarding their potential ecological function, are needed. A key concept for organizing ecological functions is the niche, the set of strategies that enable a population to persist and define its impacts on the surroundings. Here we present a framework based on manifold learning, to organize genomic information into potentially occupied bacterial metabolic niches over time. Manifold learning tries to uncover low-dimensional data structures in high-dimensional datasets, that can be used to describe the data in reduced dimensions. We apply the method to re-construct the dynamics of putatively occupied metabolic niches using a long-term bacterial time-series from the Baltic Sea, the Linnaeus Microbial Observatory (LMO). The results reveal a relatively low-dimensional space of occupied metabolic niches comprising groups of taxa with similar functional capabilities. Time patterns of occupied niches were strongly driven by seasonality. Some metabolic niches were dominated by one bacterial taxon whereas others were occupied by multiple taxa, depending on season. These results illustrate the power of manifold learning approaches to advance our understanding of the links between community composition and functioning in microbial systems.IMPORTANCEThe increase in data availability of bacterial communities highlights the need for conceptual frameworks to advance our understanding of these complex and diverse communities alongside the production of such data. To understand the dynamics of these tremendously diverse communities, we need tools to identify overarching strategies and describe their role and function in the ecosystem in a comprehensive way. Here, we show that a manifold learning approach can coarse grain bacterial communities in terms of their metabolic strategies and that we can thereby quantitatively organize genomic information in terms of potentially occupied niches over time. This approach therefore advances our understanding of how fluctuations in bacterial abundances and species composition can relate to ecosystem functions and it can facilitate the analysis, monitoring and future predictions of the development of microbial communities.

Bacterial Communities Associated with Houseflies (Musca domestica L.) Inhabiting Hospices in South Africa

Houseflies are alleged reservoirs as well as vectors of human and animal pathogens, including bacteria, because they frequently have contact with animal excreta and decaying organic substances. The rapid adaptation process of ingested microbes in the insect gut may involve gene transfer, including antibiotic resistance determinants among different bacterial strains. Six hundred and fifty-seven (n = 657) houseflies were collected from hospices and were identified morphologically and genetically using the 16S rRNA, CO1, and ITS2 barcoding genes. This study also characterized the bacterial communities harboured by the captured houseflies using 16S rRNA metabarcoding on the next-generation sequencing (NGS) platform and further sought to detect antibiotic resistance traits by using gene-specific PCR assays. Generated sequences for the targeted gene fragments matched with Musca domestica and all the sequences were deposited to the GenBank database. The 16S rRNA metabarcoding analysis revealed that the most abundant phyla detected with variable abundance observed among all the houseflies were Proteobacteria, followed by Firmicutes, and Bacteroidetes. Furthermore, the NGS data revealed the presence of multiple bacterial genera, including Providencia, Enterobacter, Dysgonomonas, Escherichia-Shigella, Klebsiella, Pseudomonas, and Streptococcus, which are known to harbour potentially pathogenic species of animals and humans. Antibiotic resistance genes detected from the housefly DNA in this study included ermB, tetA, blaSHV, and blaTEM. Moreover, these genes are associated with resistance to erythromycin, tetracycline, and beta-lactams antibiotics, respectively. The presence of bacterial pathogens and the detection of antibiotic resistance genes from the houseflies collected from the hospices indicates the possible health risk to patients in hospices and the surrounding community. Therefore, it is imperative to keep high standards of hygiene, food preparation, safety, and control of houseflies in hospices.

Taxonomic and functional responses of soil and root bacterial communities associated with poplar exposed to a contamination gradient of phenanthrene

Polycyclic aromatic hydrocarbon (PAH) contamination of industrial wasteland soils affects microbial diversity, but little is known about the dose-response effects of such contaminants on taxonomic and functional diversities of rhizospheric and plant endophytic bacteria. This study focused on the response of soil and root bacterial communities associated to poplar grown in a contamination gradient of phenanthrene (PHE). It was hypothesized that the increase in contamination would modify gradually the bacterial diversity and functions. The effects of the PHE contamination were limited to soil communities and did not affect the poplar root endophytome where Streptomyces and Cutibacterium were the most abundant genera. Along the PHE gradient, alpha-diversity indices decreased and the community structure of soil bacteria at the taxonomic level shifted. The abundance of genes involved in PAH-degradation pathways and the relative proportion of certain microbial taxa such as Polaromonas, Sphingopyxis, Peredibacter, Phenylobacterium, Ramlibacter, Sphingomonas, Pseudomonas, often described as potential PAH biodegraders, increased with the PHE concentration in the soil community. Conversely, the contamination negatively impacted other taxa like Nocardioides, Streptomyces, Gaiella, Solirubrobacter, Bradyrhizobium and Nitrospira. Functional inference and enzymatic activity measurements revealed that some bacterial functions related to carbon, nitrogen and phosphorus cycles were modified in soil throughout the PHE gradient. This study allowed a deeper understanding of the complex plant-bacteria interactions in the case of soil PAH contamination and the potential impact on soil functioning.

Bacterial Microbiota of Ostreobium, the Coral-Isolated Chlorophyte Ectosymbiont, at Contrasted Salinities

Microscopic filaments of the siphonous green algae Ostreobium (Ulvophyceae, Bryopsidales) colonize and dissolve the calcium carbonate skeletons of coral colonies in reefs of contrasted salinities. Here, we analyzed their bacterial community's composition and plasticity in response to salinity. Multiple cultures of Pocillopora coral-isolated Ostreobium strains from two distinct rbcL lineages representative of IndoPacific environmental phylotypes were pre-acclimatized (>9 months) to three ecologically relevant reef salinities: 32.9, 35.1, and 40.2 psu. Bacterial phylotypes were visualized for the first time at filament scale by CARD-FISH in algal tissue sections, within siphons, at their surface or in their mucilage. Ostreobium-associated microbiota, characterized by bacterial 16S rDNA metabarcoding of cultured thalli and their corresponding supernatants, were structured by host genotype (Ostreobium strain lineage), with dominant Kiloniellaceae or Rhodospirillaceae (Alphaproteobacteria, Rhodospirillales) depending on Ostreobium lineage, and shifted Rhizobiales' abundances in response to the salinity increase. A small core microbiota composed of seven ASVs (~1.5% of thalli ASVs, 19-36% cumulated proportions) was persistent across three salinities in both genotypes, with putative intracellular Amoebophilaceae and Rickettsiales_AB1, as well as Hyphomonadaceae and Rhodospirillaceae also detected within environmental (Ostreobium-colonized) Pocillopora coral skeletons. This novel knowledge on the taxonomic diversity of Ostreobium bacteria paves the way to functional interaction studies within the coral holobiont.

Coupling temperature-dependent spatial turnover of microbes and plants using the metabolic theory of ecology

There is an urgent need to understand the coupled relationship between belowground microbes and aboveground plants in response to temperature under climate change. The metabolic theory of ecology (MTE) provides a way to predict the metabolic rate and species diversity, but the spatial scale dependence and connections between plants and microorganisms are still unclear. Here, we used two independent datasets to address this question. One is from comprehensive sampling of paddy fields targeting bacteria and microbial functional genes, and the other is a global metadata of spatial turnover for microorganisms (bacteria, fungi and archaea, n = 139) and plants (n = 206). Results showed that spatial turnover of bacterial communities and microbial functional genes increased with temperature and fitted MTE. Through meta-analysis, the temperature-dependent spatial scale pattern was further extended to the global scale, with the spatial turnover of microorganisms and plants being consistent with MTE. Belowground microorganisms and aboveground plants were closely linked with each other even when controlling for temperature, suggesting that factors other than shared relationships with temperature also contribute to their linkages. These results implied a broad application of MTE in biology and have important implications for predicting the ecological consequences of future climate warming.

Legacy Effects of Phytoremediation on Plant-Associated Prokaryotic Communities in Remediated Subarctic Soil Historically Contaminated with Petroleum Hydrocarbons

Phytoremediation of petroleum hydrocarbons in subarctic regions relies on the successful establishment of plants that stimulate petroleum-degrading microorganisms, which can be challenging due to the extreme climate, limited nutrients, and difficulties in maintaining sites in remote locations. A long-term phytoremediation experiment was initiated in Alaska in 1995 with the introduction of grasses and/or fertilizer to petroleum hydrocarbon (PHC)-contaminated soils that were subsequently left unmanaged. In 2011, the PHC concentrations were below detection limits in all soils tested and the originally planted grasses had been replaced by volunteer plant species that had colonized the site. Here, we sought to understand how the original treatments influenced the structure of prokaryotic communities associated with plant species that colonized the soils and to assess the interactions between the rhizospheric and endophytic communities of the colonizing vegetation 20 years after the experiment was established. Metataxonomic analysis performed using 16S rRNA gene sequencing revealed that the original type of contaminated soil and phytoremediation strategy influenced the structure of both rhizospheric and endophytic communities of colonizing plants, even 20 years after the treatments were applied and following the disappearance of the originally planted grasses. Our findings demonstrate that the choice of initial phytoremediation strategy drove the succession of microorganisms associated with the colonizing vegetation. The outcome of this study provides new insight into the establishment of plant-associated microbial communities during secondary succession of subarctic areas previously contaminated by PHCs and indicates that the strategies for restoring these ecosystems influence the plant-associated microbiota in the long term. IMPORTANCE Subarctic ecosystems provide key services to local communities, yet they are threatened by pollution caused by spills and disposal of petroleum waste. Finding solutions for the remediation and restoration of subarctic soils is valuable for reasons related to human and ecosystem health, as well as environmental justice. This study provides novel insight into the long-term succession of soil and plant-associated microbiota in subarctic soils that had been historically contaminated with different sources of PHCs and subjected to distinct phytoremediation strategies. We provide evidence that even after the successful removal of PHCs and the occurrence of secondary succession, the fingerprint of the original source of contamination and the initial choice of remediation strategy can be detected as a microbial legacy in the rhizosphere, roots, and shoots of volunteer vegetation even 2 decades after the contamination had occurred. Such information needs to be borne in mind when designing and applying restoration approaches for PHC-contaminated soils in subarctic ecosystems.

Impacts of agroecological practices on soil microbial communities in experimental open-field vegetable cropping systems

This study aimed to determine the impact of different agroecological practices on the composition and diversity of edaphic bacterial and fungal communities. We designed two experimental agroecological vegetable cropping systems and analyzed their effects on soil microbial communities by pyrosequencing the 16S and 18S ribosomal RNA genes. Our results highlighted modifications to the Operational Taxonomic Units in both experimental systems compared with bare soil, particularly for the phyla Actinobacteria, Ascomycota, Bacteroidetes, and Mucoromycota. Multidimensional scaling plots based on beta diversity showed a clear distinction between the two experimental systems for fungi, whereas differences were observed between bare soil and the two experimental systems for bacteria. Overall, the agroecological systems enhanced soil microbial diversity. We showed a distinction between the two experimental systems and bare soil, correlated with the high total N and total P contents in the agroecological systems. Both experimental systems promoted soil enrichment with certain essential minerals. The agroecological systems had a positive impact on soil microbial communities, particularly by promoting the development of beneficial soil bacteria like Actinobacteria. In the two experimental systems, changes in the quality and quantity of organic matter (i.e. mulch, vermicompost, plant diversity) could have modified the abundance and diversity of microbial communities.

Buchnera breaks the specialization of the cotton-specialized aphid (Aphis gossypii) by providing nutrition through zucchini

The cotton aphid, Aphis gossypii Glover, is a species of polyphagous aphid with many biotypes, and its host transfer has always been the focus of research on the control of cotton aphid. An important factor affecting aphid specialization is the nutritional association with microbial symbionts that provide the host with nutrients lacking in the diet. We analyzed the microbial composition and biodiversity of reared on zucchini for 10 generations (T1-T10) and cotton as a control (CK), by high-throughput Illumina sequencing of 16S ribosomal RNA genes. The findings showed that the change in plant hosts decreased the richness and variety of microbial species. Regardless of whether the plant host is altered or not, Proteobacteria and Firmicutes are the predominate phyla in cotton-specialized aphid. Additionally, cotton-specialized aphids that live in zucchini had considerably lower relative abundances of non-dominant phyla (Bacteroidetes) than cotton hosts. At the genus level the dominant communities were Buchnera, Acinetobacter, and Arsenophonus. The relative abundance of Buchnera was significantly higher in aphids reared on zucchini than those on cotton, whereas the opposite was observed for Acinetobacter, as well as for some non-dominant communities (Stenotrophomonas, Pseudomons, Flavobacterium, Novosphingobium). Collectively, this study clarifies the dynamic changes of symbiotic bacteria in cotton-specialized aphids reared on zucchini for multiple generations. Among them, Buchnera is crucial for the cotton-specialized aphid to get nutrients during the transfer of the host and has a favorable impact on the colonization of cotton-specialized aphid populations on zucchini hosts. It not only enriches our understanding of the relationship between the bacterial microbiota of aphids and their adaptability to new hosts, zucchini, but also expands the current body of research on the mechanisms underlying the host shifting ability of cotton-specialized aphids.

16S-rRNA-Based Metagenomic Profiling of the Bacterial Communities in Traditional Bulgarian Sourdoughs

Sourdoughs (SDs) are spontaneously formed microbial ecosystems composed of various species of lactic acid bacteria (LAB) and acid-tolerant yeasts in food matrices of cereal flours mixed with water. To date, more than 90 LAB species have been isolated, significantly impacting the organoleptic characteristics, shelf life, and health properties of bakery products. To learn more about the unique bacterial communities involved in creating regional Bulgarian sourdoughs, we examined the metacommunities of five sourdoughs produced by spontaneous fermentation and maintained by backslopping in bakeries from three geographic locations. The 16S rRNA gene amplicon sequencing showed that the former genus Lactobacillus was predominant in the studied sourdoughs (51.0-78.9%). Weissella (0.9-42.8%), Herbaspirillum (1.6-3.8%), Serratia (0.1-11.7%), Pediococcus (0.2-7.5%), Bacteroides (0.1-1.3%), and Sphingomonas (0.1-0.5%) were also found in all 5 samples. Genera Leuconostoc, Enterococcus, Bacillus, and Asaia were sample-specific. It is interesting to note that the genus Weissella was more abundant in wholegrain samples. The greatest diversity at the species level was found in the former genus Lactobacillus, presented in the sourdough samples with 13 species. The UPGMA cluster analysis clearly demonstrated similarity in species' relative abundance between samples from the same location. In addition, we can conclude that the presence of two main clusters-one including samples from mountainous places (the cities of Smolyan and Bansko) and the other including samples from the city of Ruse (the banks of the Danube River)-may indicate the impact of climate and geographic location (e.g., terrain, elevation, land use, and nearby water bodies and their streams) on the abundance of microbiome taxa. As the bacterial population is crucial for bread standardization, we expect the local bakery sector to be interested in the relationship between process variables and their effect on bacterial dynamics described in this research study.