Differences In Community Structure Research Articles

Distribution and environmental drivers of macrofaunal nematode communities across gradients of methane seepage at cold seeps on Hikurangi Margin (New Zealand) and potential implications of disturbance from gas hydrate extraction

Cold seeps are areas characterised by specialized biological communities that rely on chemosynthesis for their nutrition. To date, research conducted on New Zealand’s Hikurangi Margin seep communities has focused on communities at 650-1200 m water depth. Here, we characterize the macrofaunal nematode communities of New Zealand cold seeps for the first time, and at deeper (> 1200 m) seep locations (Maungaroa, Glendhu and Urutī South). There were no significant difference in nematode abundance, species richness, diversity and evenness among the seep areas, which may reflect the lack of difference in most sediment variables. However, a consistent spatial pattern in nematode abundance was observed within all the seep areas on the Hikurangi Margin: abundance was highest at or near the seep centre, decreased steeply away from the centre and was low in the periphery. These spatially consistent patterns reflect the influence of methane seepage, which appears limited to the inner 150-200 m radius of each area, on nematode abundance via input of chemosynthetic food sources. We found significant differences in nematode community structure among all three areas, with most of the heterogeneity in community structure between the shallow Urutī South area and deeper Maungaroa and Glendhu areas, and differences among nematode communities of high, medium and low abundance associated with site-specific gradients in methane seepage. Within area variability in nematode community structure was mainly correlated with food availability and sediment grain size. Consistent with previous investigations of seep nematodes, we did not find evidence of seep endemics. Although deposit feeders were generally the most abundant feeding group, there were differences in the relative abundances of different feeding groups such as microvores and epigrowth feeders among the seep areas, and as a function of distance from the centre of the seep areas. Impact on seep communities from gas hydrate extraction processes may occur via reduction or potentially cessation of free-gas methane supply to the seafloor, ‘sand’ production at the seafloor due to the physical degradation of the substrate structure, or alteration of the structural integrity of the seafloor substrate. Any spatial management options considered for managing these impacts should reflect the differences in benthic community structure between depths and locations on the Hikurangi Margin.

Spatio-Temporal Change of Skin and Oral Microbiota: A Longitudinal Study of Microbial Diversity and Stability.

The human skin and oral cavity harbor complex microbial communities, which exist in dynamic equilibrium with the host's physiological state and the external environment. This study investigates the microbial atlas of human skin and oral cavities using samples collected over a 10-month period, aiming to assess how both internal and external factors influence the human microbiome. We examined bacterial community diversity and stability across various body sites, including palm and nasal skin, saliva, and oral epithelial cells, during environmental changes and a COVID-19 pandemic. The skin microbiome was confirmed to display spatial and temporal stability compared to the oral microbiome, particularly the oral epithelium, which was susceptible to changes in the host's physiological state and immune response. Moreover, significant differences in the microbial community structure among the 4 sample types were observed, and 87 distinct bacteria biomarkers were identified. The random forest prediction model achieved an overall prediction accuracy of 95.24% across the four types of samples studied. Additionally, nasal skin samples showed significant promise for individual identification through profiling the skin microbiota. These findings highlight the potential of skin and oral microbiota as forensic markers for inferring body sites and identifying individuals. In summary, despite facing limitations such as a small cohort size and the need for broader validation, this research provides an overall perspective and initial insights for refining experimental designs and conducting in-depth research in various microbial research fields.

Distribution patterns and community assembly processes of bacterial communities across different sediment habitats of subsidence lakes.

Subsidence lakes, formed due to extensive underground coal mining activities, present both ecological challenges and opportunities for alternative land use practices, such as photovoltaic power generation and aquaculture. However, the ecological consequences of these anthropogenic activities on bacterial communities within subsidence lakes remain largely unexplored. To address this knowledge gap, we conducted a comprehensive investigation of bacterial communities in two typical subsidence lake districts located in Huainan, Anhui Province, China. A total of 44 sediment samples were collected across four distinct habitats: photovoltaic zones (PV), aquaculture zones (AC), photovoltaic-aquaculture zones (PV_AC), and unimpacted zones (Natural). Bacterial communities were investigated using 16S rRNA gene sequencing and various statistical methods. Our results revealed that the α-diversity and network complexity of bacterial communities in PV, PV_AC, and AC habitats are significantly higher than habitats of Natural (P<0.01). Specifically, the α-diversity is the highest in PV habitats, while the network complexity is the highest in AC habitats. The network stability is the highest in PV and PV_AC habitats, while it is the lowest in AC. There were also significant differences in community structure among different habitats, Nitrospirota in PV (31.9%) was higher than that in the other three habitats, the percentage of Firmicute in Natural (21.96%) and PV_AC (13.70%) was higher than other two habitats, Actinobacteriota has the highest proportion in AC (20.93%). Furthermore, stochastic processes dominate community assembly in PV, PV_AC, and AC habitats, it has the highest proportion in PV, particularly on dispersal limitation (DL). However, deterministic processes prevail in Natural habitats, particularly on heterogeneous selection (HeS). Collectively, these findings highlight the significant differences in sediment bacterial communities across various habitats in subsidence lakes. Our study provides valuable insights into understanding the ecological implications of different habitats in subsidence lake ecosystems.

Effects of the Oral Health Promotion Program on oral health and oral microbiota changes in diabetic elderly individuals: a quasi-experimental study

BackgroundDiabetes with its highly prevalence has become a major contributor to the burden of health care costs worldwide. Recent unequivocal evidence has revealed a bidirectional link between oral health and diabetes. In this study, the effects of the Oral Health Promotion Program (OHPP) on oral hygiene, oral health-related quality of life and glycated haemoglobin (HbA1c) levels in diabetic elderly were examined. Moreover, microbial changes in the saliva microbiota community were also emphatically investigated.MethodsA quasi-experiment was conducted in regionally representative communities to assess oral health and oral microbiota of the elderly diabetic participants. The participants in the intervention group (n = 26) received OHPP including three phases of cognition, intensification and consolidation during the program, when those in the control group (n = 26) received routine oral care. Clinical parameters were recorded at two different time points as before the study (T0), and 3 months after intervention onset (T1). Oral health was measured via the oral health impact profile (OHIP-14) questionnaire, dental plaque index, HbA1c and mastery of oral health knowledge, and sequencing of the 16S rRNA gene from saliva samples was used to analyze the oral microbiota.ResultsThe average age of the final sample was 71.77 years (SD = 6.06), 53.8% (28/52) of whom were male. A reduction in the plaque index and improvements in oral health-related quality of life and mastery of oral health knowledge were observed in the intervention group. Meanwhile, the α-diversity of the microbiota increased in both groups, but more significant in the intervention group. PCoA analyses showed significant differences in microbial community structure in both groups, and LEfSe analyses revealed a decrease of g_Streptococcus and g_Rothia after the implementation of OHPP and a decrease of g_Streptococcusa, g_Porphyromonas, g_Gemella after the routine oral care. There was no statistically significant difference in the HbA1c level between two groups.ConclusionsOHPP superiorly contributes to the improvement of oral health and oral microbiota in elderly diabetic patients. The overarching goal is to introduce attention to the importance of good oral health as a crucial point in preventing and managing diabetes mellitus and thereby make it a meaningful contribution to public health and geriatric care.Trial registrationThis study was retrospectively registered in Chinese Clinical Trial on October 9, 2022 (ID ChiCTR2200064453).

Effects of reduced flow gradient on benthic biofilm communities' ecological network and community assembly.

The intensification of human activities has led to flow reduction and cut-off in most global rivers, seriously affecting riverine organisms and the biogeochemical processes. As key indicators of river ecosystems' structure and function, benthic biofilms play a critical role in driving primary production and material cycling in rivers. This research aimed to investigate the characteristics of microbial communities' complexity and stability during river flow reduction. Benthic biofilms were grown in artificial channels and subjected to eight gradients of flow reduction (represented by flow velocity from 0.4 to 110cm/s). Biofilms' biodiversity, ecological networks and community assembly of bacteria, fungi and algae were investigated by high-throughput sequencing. Results showed significant differences in community composition and structure under different flow conditions. The eight flow gradients' microbial communities were divided into three groups: low, medium and high flows. The flow reduction led to significant decreases in bacterial and fungal communities' Chao1 index. Low flow conditions enriched the bacterial phyla Oxyphotobacteria, Alphaproteobacteria and Mollicutes, but significantly decreased the fungal phylum Chytridiomycota. Lowering flow reduced the fungal network's number of nodes and increased the algal network's number of edges. Cross-domain interactions network analysis showed a gradual increase in node and edge numbers with decreasing flow, while decreasing average path length. The neutral model predicted stochastic processes primarily drove biofilm community assembly, and that model's explanations decreased as the flow gradient decreased. The null model analysis revealed diffusion limitation as the most common stochastic ecological process for bacterial and algal communities, with reduced flow reducing heterogeneous selection and increasing diffusion-limited processes. This study provides an in-depth analysis of flow reduction's effects on biofilm communities' ecological networks and community assembly.

Soil polluted system shapes endophytic fungi communities associated with Arundo donax: a field experiment.

With the expansion of the mining industry, environmental pollution from microelements (MP) and red mud (RM) has become a pressing issue. While bioremediation offers a cost-effective and sustainable solution, plant growth in these polluted environments remains difficult. Arundo donax is one of the few plants capable of surviving in RM-affected soils. To identify endophytic fungi that support A. donax in different contaminated environments and to inform future research combining mycorrhizal techniques with hyperaccumulator plants, we conducted a field experiment. The study compared endophytic fungal communities in A. donax grown in uncontaminated, MP soils contaminated with cadmium (Cd), arsenic (As), and lead (Pb), and RM-contaminated soils. Our findings showed that soil nutrient profiles differed by contamination type, with Cd concentrations in MP soils exceeding national pollution standards (GB 15168-2018) and RM soils characterized by high aluminum (Al), iron (Fe), and alkalinity. There were significant differences in the endophytic fungal community structures across the three soil types (p < 0.001). Co-occurrence network analysis revealed that endophytic fungi in MP soils exhibited competitive niche dynamics, whereas fungi in RM soils tended to share niches. Notably, Pleosporales sp., which accounted for 18% of the relative abundance in RM soils, was identified as a dominant and beneficial endophyte, making it a promising candidate for future bioremediation efforts. This study provides valuable insights into the role of endophytic fungi in phytoremediation and highlights their potential as resources for improving plant-microbe interactions in contaminated environments.

Soil Microbial Responses to Varying Environmental Conditions in a Copper Belt Region of Africa: Phytoremediation Perspectives

The mining industry in the copper belt region of Africa was initiated in the early 1900s, with copper being the main ore extracted to date. The main objectives of the present study are (1) to characterize the microbial structure, abundance, and diversity in different ecological conditions in the cupriferous city of Lubumbashi and (2) to assess the metal phytoextraction potential of Leucaena leucocephala, a main plant species used in tailing. Four ecologically different sites were selected. They include a residential area (site 1), an agricultural dry field (site 2), and an agricultural wetland (site 3), all located within the vicinity of a copper/cobalt mining plant. A remediated tailing was also added as a highly stressed area (site 4). As expected, the highest levels of copper and cobalt among the sites studied were found at the remediated tailing, with 9447 mg/kg and 2228 mg/kg for copper and cobalt, respectively. The levels of these metals at the other sites were low, varying from 41 mg/kg to 579 mg/kg for copper and from 4 mg/kg to 110 mg/kg for cobalt. Interestingly, this study revealed that the Leucaena leucocephala grown on the remediated sites is a copper/cobalt excluder species as it accumulates soil bioavailable metals from the rhizosphere in its roots. Amplicon sequence analysis showed significant differences among the sites in bacterial and fungal composition and abundance. Site-specific genera were identified. Acidibacter was the most abundant bacterial genus in the residential and remediated tailing sites, with 11.1% and 4.4%, respectively. Bacillus was predominant in both dry (19.3%) and wet agricultural lands (4.8%). For fungi, Fusarium exhibited the highest proportion of the fungal genera at all the sites, with a relative abundance ranging from 15.6% to 20.3%. Shannon diversity entropy indices were high and similar, ranging from 8.3 to 9 for bacteria and 7.0 and 7.4 for fungi. Β diversity analysis confirmed the closeness of the four sites regardless of the environmental conditions. This lack of differences in the microbial community diversity and structures among the sites suggests microbial resilience and physiological adaptations.

Exploring the Correspondence Between Benthic Algae and Changes in the Aquatic Environment for Biodiversity Development

In order to promote the development of biodiversity, the present study conducted three sampling surveys at 26 representative sampling sites selected from the Chishui River, a freshwater river in China, in July (rainy season), November (flat water period), and April 2024 (dry season), respectively, focusing on the relationship between benthic algae and the response of water environmental factors. The results revealed that a total of 140 species from 48 genera and 7 phyla of benthic algae were identified, with the highest number of species belonging to the diatom phylum (85 species). The average density of benthic algae was highest during the flat water period, followed by the dry season and the flood season. Microcystis sp. was the dominant species during the flood season, while Gomphonema sp., Achnanthes tumescens, and Oscillatoria sp. were common dominant species during the dry and flat water periods. Achnanthes tumescens was the absolute dominant species in the upstream during the dry and flat water periods; Leptolyngbya sp. was the absolute dominant species in the midstream during the flat water period, and Oscillatoria sp. was the absolute dominant species in the middle reaches during the dry season. The Shannon-Wiener index, Margalef index, and species richness of benthic algae during the dry and flat water periods decreased from upstream to downstream. Non-metric multidimensional scaling analysis revealed significant differences in the community structures of benthic algae in the upper, middle, and downstream areas of the Chishui River during different periods, while cluster analysis indicated high similarity among benthic algae communities in locally adjacent areas. The differences in the benthic algae community structure increased with environmental and geographical distance, with environmental distance playing a greater role than geographical distance. RDA (Redundancy Analysis) identified TN (Total Nitrogen), TP (Total Phosphorus), DO (Dissolved Oxygen), EC (Electrical Conductivity), and NH3-N (Ammonia Nitrogen) as key water environmental factors influencing the structure of benthic algal communities in the Chishui River.

Environmental sex reversal in parrotfish does not cause differences in the structure of their gut microbial communities

Parrotfish are a common fish in coral reef areas, but little is known about their gut microbial communities. In addition, parrotfish are capable of sex reversal, usually some males are sexually reversed from females, and it is still not known whether this sex reversal leads to significant changes in gut microbial communities. In this study, we investigated the gut microbial communities of three species of parrotfish including Scarus forsteni (4 females and 4 sex-reversed males), Scarus ghobban (5 females and 5 sex-reversed males), and Hipposcarus longiceps (5 females and 5 sex-reversed males) by using high-throughput sequencing technology. The gut microbial communities of these three species were mainly composed of Pseudomonadota (class Gammaproteobacteria) and Bacillota, while at the family level, they mainly included Vibrionaceae, Burkholderiaceae, Enterobacteriaceae, Streptococcacea, and Erwiniaceae. Although at the genus level, there were a large number of unclassified lineages, the remaining gut microorganisms were mainly composed of Vibrio, Photobacterium, Enterococcus and Lactococcus. Furthermore, we did not find significant differences in gut microbial community structure between the female parrotfish and corresponding female reversed males within each species, even in terms of the structure of gut microbial functional information obtained from 16 S rRNA gene sequence predictions. However, the gut microbial communities of these three species of parrotfish differed significantly not only in their community structure but also in their microbial functional information structure, mainly in terms of aspartate and asparagine biosynthesis, histidine degradation, inositol degradation, heptose biosynthesis, chitin derivatives degradation, enterobactin biosynthesis, and thiazole biosynthesis. Our study provides essential gut microbial community data for understanding the physiology and sex reversal phenomenon in parrotfish.

Difference in Community Structure and Function of Bacteria Attached to Stems and Leaves of Potamogeton crispus Compared to that of Bacteria in the Overlying Water and Sediment

The stems and leaves of submerged macrophytes usually grow below the water surface and could provide a good biological carrier for the colonization and growth of planktonic bacteria in water. Therefore, attached bacteria on the stem and leaf surfaces of submerged macrophytes are important components and play a crucial role in aquatic ecosystems. To further understand the structure characteristics and functional differences of the bacterial community attached to the stems and leaves of submerged macrophytes, the submerged macrophytes Potamogeton crispus and the overlying water and sediment were sampled and analyzed in this study. The results showed that a total of 10 320 OTUs were detected in the P. crispus samples, the overlying water samples, and the sediment samples. These OTUs included 64 phyla, 189 classes, 448 orders, 721 families, and 1 366 genera. The richness and diversity of bacterial communities in sediments were the highest, followed by the stem and leaves of P. crispus, and the alpha diversity index of planktonic bacteria in water was the lowest. Significant differences （P&lt;0.05） were observed among the four alpha diversity indices of the three source samples. Bacterial communities with greater similarity were obtained from the same source samples, but there was more distinct community composition dissimilarity in bacteria collected from the submerged macrophytes and the overlying water and sediment samples （P&lt;0.05）. At the level of phylum, order, and genus classification, the relative abundance of most dominant bacterial species, non-dominant species, and occasional species showed significant differences among the three source samples （P&lt;0.05）. Proteobacteria, Actinobacteria, and Bacteroidetes were common dominant bacterial phyla for the three source samples, while Firmicutes were unique dominant phyla for attachment bacteria on the plant stem and leaves of P. crispus. There were differences in carbohydrate metabolism, energy metabolism, amino acid metabolism, cofactors, and vitamin metabolism among the three source samples （P&lt;0.05）. The relative abundance of chemical heterotrophic and oxidative heterotrophic functional types in the stem and leaf samples of P. crispus was higher than that in the overlying water and sediment samples. In addition, higher nitrate reduction, nitrogen respiration, and nitric acid respiration functions were observed in sediment samples. To summarize, the stems and leaves have the potential to encourage bacterial colonization and create a unique bacterial community on the surface of submerged macrophytes. Submerged P. crispus macrophytes and their surroundings （water and sediment） play different roles in the biogeochemical cycling of nutrients in the freshwater ecosystem.

Causal determinism by plant host identity in arbuscular mycorrhizal fungal community assembly

Abstract An assumption in ecology is that plant identity plays a central role in the assembly of root‐colonising arbuscular mycorrhizal (AM) fungal communities. While numerous correlational studies support this notion, with evidence of host selectivity among fungal taxa and host‐specific responses to different AM fungi, empirical demonstrations of host‐driven AM fungal community assembly remain surprisingly limited. We conducted a factorial experiment growing two globally significant crop species, wheat (Triticum aestivum) and sorghum (Sorghum bicolor), with a common pool of AM fungal species, or without AM fungi. We hypothesised strong differences in AM fungal community structure between the two species driven by strong habitat filtering. Plants were harvested at two time points in which we analysed the community structure of AM fungi in the roots, the phylogenetic diversity, and interactions with plant physiological responses. As we expected, there were distinct trajectories in both the composition and phylogenetic diversity of AM fungal communities between the two host plants through time. However, the effect of habitat filtering during community assembly differed between the two species. In sorghum roots, AM fungal communities exhibited increased richness and became more phylogenetically clustered over time. This shift suggests that community assembly was primarily driven by habitat filtering, or selectivity, imposed by the host which was accompanied by significant increases in plant mycorrhizal growth (from 11.83% to 43.67%) and phosphorus responses (from −0.6% to 43.3%). In contrast, AM fungal communities in wheat displayed little change in diversity, remained phylogenetically unstructured, and provided minimal benefits to the host, indicating a more stochastic assembly process with a stronger influence of competitive interactions. As the field looks to understand what determines the distribution of AM fungi and their community composition while simultaneously seeking to utilise AM fungi for ecosystem benefits, it is important to know the extent to which host identity can influence fungal assembly within plant roots. Our results provide empirical support of host‐determinism in AM fungal community assembly and suggest that this determinism is associated with the growth and nutrient benefits provided by the symbiosis to plants. Read the free Plain Language Summary for this article on the Journal blog.

Intensive monocropping of bananas decreases the soil acid buffering capacity via ammonia-oxidizing bacteria

Ammonia-oxidizing microorganisms (AOM) are vital for soil nitrogen cycling, nutrient availability, and soil health during sustainable agriculture. Long-term continuous cultivation of bananas and improper chemical fertilization affect the adaptability of AOM; however, the underlying basis for this phenomenon is unclear. This study utilized 16S rRNA gene and metagenomic sequencing techniques to examine soil from banana plantations that were continuously cultivated for 2, 3, 7, 10, 12, and 13 years (Y2, Y3, Y7, Y10, Y12, and Y13, respectively). The results indicated a significant decrease in soil acidity buffering capacity (pHBC) with increasing years of continuous cropping. Furthermore, compared with forest soil (Y0), Y7, Y10, Y12, and Y13 soils exhibited a significantly increased potential nitrification rate (PNR) as well as an abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB), with no significant difference in complete ammonia oxidizers (comammox). Principal component analysis (PCA) further demonstrated marked differences in chemical properties and ammonia-oxidizing microbial community structures between the soils under long-term (Y7, Y10, Y12, Y13) and short-term (Y2, Y3) banana cultivation. In addition, metagenome analysis results indicated that the relative abundance of Nitrososphaera-AOA and Ca. Nitrosocosmicus-AOA as well as Nitrosospira-AOB, Nitrosovibrio-AOB, Nitrosomonas-AOB, and comammox Nitrospira jacus was significantly higher in Y7 and Y13 soils than in Y0 controls. Redundancy analysis (RDA) identified pHBC, CEC, and NH4+ as the primary chemical factor responsible for the differences in AOM microbial communities, whereas random forest analysis revealed that Nitrosospira-AOB significantly contributed to PNR. In summary, long-term continuous banana cultivation primarily stimulates AOB promote soil ammonia oxidation, leading to soil acidification.Graphical

Microbial Community Structure, Diversity, and Succession During Decomposition of Kiwifruit Litters with Different Qualities.

There are differences in the litter quality and decomposition rate of kiwifruit varieties, but it is not clear whether these differences are related to microbial communities. The leaf litters of two kiwifruit varieties (A. chinensis cv 'Hongyang' and A. chinensis cv 'Jinyan') were taken as objects, and the structure, diversity, and succession of the soil microbial communities were analyzed using an in situ decomposition experiment. Moreover, the contents of C, N, P, and K in the litters during decomposition were analyzed. The results show that there were variety differences in community structure at the generic level. Lophotrichus, Acaulium, and Fusarium were relatively more abundant in the microbial community of the 'Hongyang' kiwifruit litter, and Humicola and Tausonia were relatively more abundant in the microbial community of the 'Jinyan' kiwifruit litter. Subgroup_6 and Sphingomonas were the dominant bacteria. The bacterial community diversity of 'Jinyan' kiwifruit was higher than that of the 'Hongyang' kiwifruit litter. The community diversity was higher in the middle and later periods. The contents of C and N in the litters were the main factors affecting microbial communities. The abundances of Humicola and Apiotrichum were negatively correlated with the contents of C and N, and the abundances of Sphingomonas and SC-I-84 were positively correlated with the content of C. There were variety differences in the microbial communities corresponding to the decomposition processes of the 'Hongyang' and 'Jinyan' kiwifruit litters. The mechanisms of the variety differences were related to litter quality and the initial soil microbial community.

Stable Diversity but Distinct Metabolic Activity of Microbiome of Roots from Adult and Young Chinese Fir Trees

The tree-associated microbiome is vital for both individual trees and the forest ecosystem. The microbiome is dynamic; however, it is influenced by the developmental stages and environmental stresses experienced by host trees. Chinese fir (Cunninghamia lanceolata) is an economically important tree species in the subtropical regions of China. This study investigated the diversity of microbial communities, including bacteria and fungi, in the roots and bulk soil of young (2 years old) and old (46 years old) Chinese fir. It specifically examined the functional characteristics of these microbial communities. Through a non-metric multidimensional scaling (NMDS) analysis, we examined differences in microbial community structures among root and soil samples of Chinese fir. Evaluations using α-diversity metrics (Chao1, Shannon, Pielou, etc.) confirmed significant differences in diversity and structure between soil and root samples but high similarity between young and old tree samples. A network analysis identified key bacterial and fungal genera, such as Burkholderia and Russula, which play pivotal roles in the microbiome structure. We also demonstrated significant variations in microbial metabolic functions, such as dioxin and benzoic acid degradation metabolic pathways, which might relate to stress alleviation for tree fitness. Additionally, for the detection of endophytic microorganisms in Chinese fir seeds, only small amounts (less than 10%) of fungal endophytes and bare bacterial endophytes were identified. In summary, this study revealed that the stable structure of the rhizosphere microbiome was established in the early stage of tree life in Chinese fir, which mostly originated from surrounding soil rather than seed endophytes. The associated microbial metabolic activity naturally decreased with tree aging, implicating the tree microbial dynamics and the need for the addition of an actively functional synthetic community for tree fitness.

Gut pathobiont enrichment observed in a population predisposed to dementia, type 2 diabetics of Mexican descent living in South Texas

Type 2 diabetes (T2D) is a common forerunner of neurodegeneration and accompanying dementia, including Alzheimer’s Disease (AD), yet the mechanisms underlying this comorbidity remain unresolved. Individuals of Mexican descent living in South Texas have increased prevalence of comorbid T2D and early onset AD, despite low incidence of the APOE-ε4 risk variant among the population and an absence of a similar predisposition among relatives residing in Mexico – suggesting a role for environmental factors in coincident T2D and AD susceptibility. We therefore sought to test if differences in gut community structure could be observed in this population prior to any AD diagnosis. Here, in a small clinical trial (ClinicalTrials.gov Identifier NCT04602650), we report evidence for altered gut microbial ecology among subjects of Mexican descent living in South Texas with T2D (sT2D) compared to healthy controls without T2D (HC), despite no differences in expressed dietary preferences. We performed metataxonomic 16S rRNA gene amplicon sequencing of study participant stool samples. Although no significant decrease in microbial alpha diversity was observed between sT2D gut communities versus those of HC, body mass index was identified as a driver of gut community structure. Intriguingly, we observed a significant negative association of Faecalibacterium and Lachnospiraceae with T2D and an increase in the abundance of pathobionts Escherichia-Shigella, Enterobacter, and the erysipelotrichial species Clostridia innocuum among sT2D gut microbiota, as well as differentially abundant gene and metabolic pathways. Future large-scale, longitudinal sequencing efforts of the gut microbiome of individuals with T2D who go on to develop AD might identify key actors among “disease state” microbiota that contribute to increased susceptibility to comorbid dementia. Finally, we identified candidate microbiome-targeted approaches for the treatment of T2D.

Insights into the variations in microbial community structure during the development of periodontitis and its pathogenesis.

To characterize the subgingival microbiota in subjects with stage I/II periodontitis (moderate periodontitis, MP), stage III/IV periodontitis (severe periodontitis, SP), and periodontal health (PH) at the same probing depth (PD) (shallow ≤ 3mm, moderate 4-6mm, or deep ≥ 7mm), and to investigate the changes associated with probing depth progression. 100 subgingival plaque samples were collected from 50 subjects (16 MP, 17 SP and 17 PH), forming six groups: PHS (PH, shallow), MPS (MP, shallow), MPM (MP, moderate), SPS (SP, shallow), SPM (SP, moderate), and SPD (SP, deep). Samples were analyzed using high-throughput sequencing. The subgingival microbiome showed significant differences associated with both PD and periodontitis stage (p < 0.05). With increasing PD, alpha diversity initially increased and then decreased. Pathogenic genera like Fusobacterium, Filifactor, and Porphyromonas increased, while health-associated genera like Streptococcus and Haemophilus decreased. At shallow sites, the PHS, MPS, and SPS groups showed similar community structure. At moderate and deep sites, the SPM and SPD groups exhibited significant differences in community structure compared to the MPM group, with the SPM and SPD groups showing decreased abundances of Actinomyces and increased abundances of Treponema. The microbial co-networks in the SPD and SPM groups exhibited greater complexity and connectivity and were more resilient to random microbial or node removal. The subgingival microbiome shows strong associations with PD and periodontitis stage. Once periodontitis progresses to stage III/IV, reconstructing a healthy subgingival microbiome may be challenging, emphasizing the importance of early prevention.

Differences in bacterial community structure and volatile flavor substance of industrial-scale tiger skin chicken feet stored at air packaging and vacuum packaging

The aim of this study was to investigate the differences of quality indexes, bacterial community and volatile organic compounds (VOCs) of industrial-scale tiger skin chicken feet (TSCF) under air packaging (AP) and vacuum packaging (VP). The results showed that the pH, total volatile basic nitrogen, total number of bacterial colony, and sensory scores in VP group changed less than those in AP group during the storage period. Different packaging conditions also had significant effects on bacterial community at the genus levels. Weissella and Lactococcus was the dominant genus in AP group, while Lactiplantibacillus and Pediococcus also had the large proportions in addition to Weissella and Lactococcus in VP group, which also led to the differences in VOCs between the two groups. Several VOCs could be used as potential spoilage indicators, including 2-octanone, ethanol, ethyl acetate and acetic acid in AP-stored TSCF, and 2-octanone, ethanol, ethyl acetate, 2-butyl-1-octanol, (R)-2-butanol, (E)-3-hexenoic acid and 2-butanone in VP-stored TSCF. Correlation analysis showed that these predominance spoilage microorganisms were significantly correlated with these VOCs of TSCF during the storage period. This study can provide a theoretical basis for understanding of the spoilage process of TSCF.

Rational eucalypt logging site management patterns enhance soil phosphorus bioavailability and reshape phoD-harboring bacterial community structure

Continuous planting of eucalypt plantations negatively affects soil nutrient effectiveness, especially soil phosphorus (P) availability. Therefore, exploring the response characteristics of soil P-mineralising microbial communities and the distribution mechanism of soil P fractions under different transformation patterns on eucalypts logging sites holds great practical significance for improving soil nutrient effectiveness in plantations. This experiment investigated the effects and correlations between four different transformation patterns on soil phoD-harboring bacterial communities, alkaline phosphatase (ALP) activity, and P fractions. Management patterns mainly included non-forest area formed upon eucalypt stump germination suppression after two generations of Eucalyptus afforestation (TWE), the third generation of pure plantation planting (THE), mixing of Eucalyptus with Manglietia glauca (EM), and rotation of pure M. glauca plantation (MM), with previous mixed coniferous and broadleaf forest (CK) as the control. The results showed that, TWE and THE significantly reduced soil (0–10 cm and 10–20 cm) organic carbon (SOC), total nitrogen (TN), bioavailable P, and labile Po, and increased the occluded P and ALP activity compared to CK; however, SOC, TN, bioavailable P, and labile Po indices improved in plantations of EM or MM compared to TWE and THE. Meanwhile, the four management patterns on the logging site caused significant differences in phoD gene community structure and diversity. TWE and THE significantly increased the relative abundances (RAs) of Pseudomonadaceae and Comamonadaceae, which correlated negatively with soil bioavailable P and HCl-P and positively with ALP activity, suggesting a positive effect on Po mineralization and insoluble P mobilization. In contrast, Streptomycetaceae and Oxalobacteraceae were significantly enriched in EM or MM, implying that not all microorganisms carrying phoD genes play important roles in synthesizing ALP. The structure equation model showed that TN, resin-Pi, NaHCO3-Pi, and HCl-P had indirect effects on ALP through phoD-harbouring bacterial diversity and community composition. These findings provide a basis for understanding the soil P cycling mechanism after eucalypt plantations logging site transformation.

The strong seasonality of soil microbial community structure in declining Mediterranean pine forests depends more on soil conditions than on tree vitality

The soil microbiome plays an important role in forest functioning. However, the impact of drought-induced dieback and tree death on soil microbial biomass, community structure, and functional composition is unknown. We also lack understanding on how soil microbiota varies seasonally in such declining stands. We used Phospholipid Fatty Acids (PLFA) analysis to quantify soil microbial biomass and study its seasonal changes in three Mediterranean forests showing dieback and dominated by three pine species (Pinus halepensis Mill, Pinus pinaster Ait. and Pinus sylvestris L.). We also measured microclimatic parameters and soil physical and chemical parameters under trees with different vigor, assessed as canopy defoliation degree, and related them to seasonal changes in the soil microbial community. We found marked differences in soil microbial community structure, total biomass, and the relative abundance of major functional groups among forests. First, soil microbial biomass peaked either in the dry summer (P. halepensis) or in autumn (P. pinaster and P. sylvestris). Accordingly, the relative abundance of most functional groups, excluding Arbuscular mycorrhizal fungi, displayed substantial variation between seasons. In addition, the relative abundance of fungi and Gram-positive bacteria exhibited an opposite pattern compared to actinomycetes and Gram-negative bacteria. Second, soil physical and chemical parameters had a significant impact on within-site PLFA variation, although their influence was less important than that of seasonal variation. Third, differences between defoliated and healthy trees were minor and restricted to averaged ratios between different PLFA markers. Overall, the structure, biomass and relative abundance of major functional groups of the soil microbiome vary considerably among stand types and seasons in forests showing ongoing dieback and high mortality. However, while the seasonal dynamics show predictable patterns, which should be accounted for in future studies, the within-site variation is highly variable and mainly depends on soil physical and chemical parameters.

EDNA metabarcoding reveals differences in fish diversity and community structure in Danjiang River

Fish diversity, an important indicator of aquatic ecosystem health, is declining due to water pollution, overfishing, climate change, and invasive species. Effective surveying and monitoring are required to protect fish diversity. Here, a high-sensitivity environmental DNA (eDNA) metabarcoding technique was used to investigate fish diversity in the Danjiang River, Shaanxi Province, China. In total, 59 species were identified in eight orders, 19 families, and 40 genera. Cypriniformes and Perciformes were the main groups in the survey area, while Cyprinidae accounted for 50.85% of the total fish species. Rhinogobius similis (19%), Hemibarbus umbrifer (11%), Gnathopogon herzensteini (10%), Triplophysa stewarti (8%), and Zacco platypus (7%) were the dominant species. Eight rare and two exotic fish species were identified. Combined with analysis of historical data, the richness of fish identified using eDNA metabarcoding was significantly higher than that of fish captured in ground cages. Temperature, pH, and oxidation-reduction potential are the main environmental factors that affect the spatial distribution of fish communities. These results suggest that eDNA metabarcoding could be a new tool with broad application prospects; however, local databases must be improved. This study provides theoretical data and a methodological reference for protecting and managing fish diversity in the Qinling Mountains.