Intensive ecological interventions have been carried out in highly polluted shallow lakes to improve their environments and restore their ecosystems. However, certain treatments, such as dredging polluted sediment and stocking fish, can impact the aquatic communities, including benthos and fishes. These impacts can alter the composition and characteristics of aquatic communities, which makes community-based ecological assessments challenging. Here we develop a bacteria-based index of biotic integrity (IBI) that can clearly indicate the restoration of aquatic ecosystems with minimal artificial interventions. We applied this method to a restored shallow lake during 3-year intensive ecological interventions. The interventions reduced nutrients and heavy metals by 27.1% and 16.7% in the sediment, while the total organic carbon (TOC) increased by 8.0% due to the proliferation of macrophytes. Additionally, the abundance of sulfur-related metabolic pathways decreased by 10.5% as the responses to improved ecosystem. The score of bacteria-based IBI, which is calculated based on the diversity, composition, and function of benthic bacterial communities, increased from 0.62 in 2018 to 0.81 in 2021. Our study not only provides an applicable method for aquatic ecological assessment under intensive artificial interventions but also extends the application of IBI to complex application scenarios, such as ecosystems with significantly different aquatic communities and comparisons between different basins.

BACKGROUND: The gut morphology of Symphalangus syndactylus exhibits an intermediate structure that aligns with its consumption of fruit and ability to supplement its diet with leaves. The Siamang relies on its gut microbiome for energy extraction, immune system development, and the synthesis of micronutrients. Gut microbiome composition may be structured based on several factors such as age, sex, and habitat. No study has yet been carried out on the gut microbiota of the Hylobatidae members in Malaysia especially S. syndactylus.
METHODS: This study aims to resolve the gut microbiome composition of S. syndactylus by using a fecal sample as DNA source, adapting high-throughput sequencing, and 16S rRNA as the targeted region.
RESULTS: A total of 1 272 903 operational taxonomic units (OTUs) reads were assigned to 22 phyla, 139 families, and 210 genera of microbes. The {Unknown Phylum} Bacteria-2 is the dominant phyla found across all samples. Meanwhile, {Unknown Phylum} Bacteria-2 and Firmicutes are genera that have the highest relative abundance found in the Siamang gut.
CONCLUSIONS: This study yields nonsignificance relationship between Siamang gut microbiome composition with these three factors: group, sex, and age.

Hydrogen-rich water (HRW) is a beverage containing a high concentration of hydrogen that has been researched for its antioxidant, anti-apoptotic, and anti-inflammatory properties in asthma. This study investigates the potential therapeutic impact of HRW on the gut-lung axis. Using 16S rRNA and serum metabolomics, we examined changes in gut microbiota and serum metabolites in asthmatic mice after HRW intervention, followed by validation experiments. The findings revealed that HRW influenced gut microbiota by increasing Ligilactobacillus and Bifidobacterium abundance and enhancing the presence of indole-3-acetic acid (IAA), a microbially derived serum metabolite. Both in vivo and in vitro experiments showed that HRW\'s protective effects against airway inflammation in asthmatic mice may be linked to the gut microbiota, with IAA potentially playing a role in reducing asthmatic airway inflammation through the aryl hydrocarbon receptors (AhR) signaling pathway. In summary, HRW can modify gut microbiota, increase Bifidobacterium abundance, elevate microbial-derived IAA levels, and activate AhR, which could potentially alleviate inflammation in asthma.

Petroleum hydrocarbons are being released into the marine environment continuously. They will undergo weathering and may eventually be biodegraded by bacteria and other microbes. While nanoplankton (2-20 μm) are the major consumers of marine bacteria, their effect on the process of biodegradation of oil hydrocarbons is still debated. A 14-day microcosm experiment was conducted to investigate the effects of crude oil hydrocarbons on nanoplankton bacterivory and bacterial community in coastal waters. The coefficients of population growth (0.56-1.80 d-1 for all treatments considered) and grazing mortality (0.38-1.65 d-1 for all treatment considered) of bacteria estimated with the dilution method did not differ among the treatments of control (Ctrl), low dose chemically dispersed oil (LDOil, 2 μL L-1 of crude oil), and high dose chemically dispersed oil (HDOil, 8 μL L-1 of crude oil). Bacterial abundance ranged between 0.21-0.86 x 106 cells mL-1 on average for all treatments. The lack of drastic increases in the cell density of bacterial cells in the oil-loaded treatments was observed throughout the experiment period. Sequencing analysis of the 16S rRNA gene revealed the progressive changes in the community compositions of the bacteria in all treatments. The relatively high abundance of oil-degrading bacteria, including Cycloclasticus and Alcanivorax on Days 3-14 of the experiment reflected the presence of biodegradation of oil in the LDOil and HDOil treatments. Throughout the 14 days, the community composition of bacteria in the LDOil and HDOil treatment became more similar and they both differed from that in the Ctrl treatment. This study concluded that, in oil-polluted seawater, the changes in the bacterial community composition were mainly resulting from the addition of chemically dispersed crude oil.

Seagrass meadows play pivotal roles in coastal biochemical cycles, with nitrogen fixation being a well-established process associated with living seagrass. Here, we tested the hypothesis that nitrogen fixation is also associated with seagrass debris in Danish coastal waters. We conducted a 52-day in situ experiment to investigate nitrogen fixation (proxied by acetylene reduction) and dynamics of the microbial community (16S rRNA gene amplicon sequencing) and the nitrogen fixing community (nifH DNA/RNA amplicon sequencing) associated with decomposing Zostera marina leaves. The leaves harboured distinct microbial communities, including distinct nitrogen fixers, relative to the surrounding seawater and sediment throughout the experiment. Nitrogen fixation rates were measurable on most days, but highest on days 3 (dark, 334.8 nmol N g-1 dw h-1) and 15 (light, 194.6 nmol N g-1 dw h-1). Nitrogen fixation rates were not correlated with the concentration of inorganic nutrients in the surrounding seawater or with carbon:nitrogen ratios in the leaves. The composition of nitrogen fixers shifted from cyanobacterial Sphaerospermopsis to heterotrophic genera like Desulfopila over the decomposition period. On the days with highest fixation, nifH RNA gene transcripts were mainly accounted for by cyanobacteria, in particular by Sphaerospermopsis and an unknown taxon (order Nostocales), alongside Proteobacteria. Our study shows that seagrass debris in temperate coastal waters harbours substantial nitrogen fixation carried out by cyanobacteria and heterotrophic bacteria that are distinct relative to the surrounding seawater and sediments. This suggests that seagrass debris constitutes a selective environment where degradation is affected by the import of nitrogen via nitrogen fixation.

UNASSIGNED: In recent decades, Caribbean coral reefs have lost many vital marine species due to diseases. The well-documented mass mortality event of the long-spined black sea urchin Diadema antillarum in the early 1980s stands out among these collapses. This die-off killed over 90% of D. antillarum changing the reefscape from coral to algal-dominated. Nearly 40 years later, D. antillarum populations have yet to recover. In early 2022, a new mortality event of D. antillarum was reported along the Caribbean, including Puerto Rico.
UNASSIGNED: This study identifies the gut microbiota changes associated with the D. antillarum during this mortality event. It contrasts them with the bacterial composition of gut samples from healthy individuals collected in 2019 by using 16S rRNA sequencing analyses.
UNASSIGNED: Notably, the die-off group\'s core microbiome resembled bacteria commonly found in the human skin and gut, suggesting potential anthropogenic contamination and wastewater pollution as contributing factors to the 2022 dysbiosis. The animals collected in 2022, especially those with signs of disease, lacked keystone taxa normally found in Diadema including Photobacterium and Propionigenium.
UNASSIGNED: The association between human microbes and disease stages in the long-spined urchin D. antillarum, especially in relation to anthropogenic contamination, highlights a complex interplay between environmental stressors and marine health. While these microbes might not be the direct cause of death in this species of sea urchins, their presence and proliferation can indicate underlying issues, such as immune depletion due to pollution, habitat destruction, or climate change, that ultimately compromise the health of these marine organisms.

UNASSIGNED: Unlike plant phytochemicals, little has been done to explore the metabolites from phyllosphere bacterial flora, some of which enabled them to survive interspecific competition through amensalism. This study evaluated the antimicrobial activity of metabolites from Phyllospheric Bacteria (PB) isolated from Funtumia elastica (FE), against selected bacterial and fungal pathogens. Phenotypic and molecular methods were used to identify the isolated phyllo-microbiota.
UNASSIGNED: The PB were aseptically isolated by sonication. Their metabolites were obtained from the fresh overnight culture of the organisms. The cell-free supernatants containing the metabolites were used for antimicrobial assays against the pathogens. The DNA of the bacterial isolates were isolated using a NIMR-BIOTECH DNA extraction kit, while their 16S rRNA was amplified with the primer: 799F 5\'-AACACGGATTA GATACC-3\', 1193R 5\'- ACGTCATCCCCACCTTCC-3\', using SolisFast* Master Mix, (Solis Biodyne-Estonia). The BLAST of the sequence was done from the NCBI Gen-bank. The PB strains identified were submitted to NCBI and accession numbers were assigned to them.
UNASSIGNED: The phyllosphere of FE yielded 21 bacterial isolates: 7 Gram-positives and 14 Gram-negatives. The metabolites from these isolates showed varying degrees of bioactivity against Staphylococcus aureus (ATCC29213), Escherichia coli (ATCC 25922) Klebsiella pneumoniae (ATCC 35659); Trychophyton rubrum, Candida albicans and Microsporum canis. Fifteen bioactive isolates sequenced yielded four genera, Enterobacter (E. hormaechei 98.44%), Bacillus (B. cereus 100%), Pontoea (P. dispersa 99.72%), Staphylococcus (S. arlettae 99.72%).
UNASSIGNED: Bacteria from FE phyllosphere, produced metabolites antagonistic (cidal) to some human pathogens. This has great potential for possible drug discovery.

A total of 231 blood samples from wild mammals belonging to the orders Rodentia (n = 142) and Didelphimorphia (n = 89) were screened by real-time PCR assay (qPCR), being six Rhipidomys sp., 118 Thrichomys laurentius, nine Rattus rattus, four Kerodon rupestris, five Necromys lasiurus, 42 Didelphis albiventris and 47 Monodelphis domestica. Results using qPCR showed that 32 of the total 231 (13.85%) samples were positive for hemoplasma sequences of the 16S rRNA gene. Sequences from two D. albiventris showed 99.77-99.89% identity with \'Candidatus Mycoplasma haemoalbiventris\' and 99.09% with \'Candidatus Mycoplasma haemodidelphidis\', respectively. Furthermore, one M. domestica and five T. laurentius showed 99.72-99.77% identity with Mycoplasma sp., and one K. rupestris showed 98.13% identity with \'Candidatus Mycoplasma haematohydrochaerus\'; and from two Rattus rattus showed 99.65-99.89% identity with Mycoplasma sp. and \'Candidatus Mycoplasma haemomuris\'. The 23S rRNA gene sequences obtained from the two D. albiventris showed 100% identity with \'Ca. M. haemoalbiventris\' whereas the sequences from the R. rattus showed only 85.31% identity with \'Candidatus Mycoplasma haematohydrochaerus\'. Two T. laurentius and one K. rupestris showed 84.66-92.97% identity with \'Candidatus Mycoplasma haemosphiggurus\'. Based on phylogenetic and Neighbor-Net network analyses of the 16S and 23S rRNA genes, potential novel species are described. In addition, \'Ca. M. haemoalbiventris\' was detected in Didelphis albiventris, and Mycoplasma sp. was detected in Rattus sp. rodents from the Caatinga biome, Brazil.

Exopolysaccharides (EPSs) are carbohydrate polymers that are synthesized and secreted into the extracellular during the growth of microorganisms. Bacillus thuringiensis (Bt) is a type of entomopathogenic bacterium, that produces various insecticidal proteins and EPSs. In our previous study, the EPSs produced by Bt strains were first found to enhance the toxicity of insecticidal crystal proteins against Plutella xylostella. However, the response of the intestinal bacterial communities of P. xylostella under the action of EPSs is still unelucidated. In this study, 16S rRNA amplicon sequencing was used to characterize the intestinal bacterial communities in P. xylostella treated with EPSs alone, Cry1Ac protoxin alone, and both the Cry1Ac protoxin and EPSs. Compared with the control group, alpha diversity indices, the Chao1 and ACE indices were significantly altered after treatment with EPSs alone, and no significant difference was observed between the groups treated with Cry1Ac protoxin alone and Cry1Ac protoxin + EPSs. However, compared with the gut bacterial community feeding on Cry1Ac protoxin alone, the relative abundance of 31 genera was significantly changed in the group treated with Cry1Ac protoxin and EPSs. The intestinal bacteria, through the oral of Cry1Ac protoxin and EPSs, significantly enhanced the toxicity of the Cry1Ac protoxin towards the axenic P. xylostella. In addition, the relative abundance of the 16S rRNA gene in the chloroplasts of Brassica campestris decreased after adding EPSs. Taken together, these results show the vital contribution of the gut microbiota to the Bt strain-killing activity, providing new insights into the mechanism of the synergistic insecticidal activity of Bt proteins and EPSs.

Sterile insect technique (SIT) is a useful strategy for preventing and mitigative establishment of invasive insect species. SIT of the pest tephritid Mediterranean fruit fly, Ceratitis capitata (Wiedemann, 1824)WiedemannWiedemann, has been effective in preventing population establishment in vulnerable agricultural areas of the United States. However, irradiation-induced sterilization can have detrimental impacts resulting in reduced performance metrics. Mediterranean fruit fly males reared for SIT have been shown to have differences in their microbiomes relative to other population sources, which has been postulated to be a factor in how well flies compete with wild conspecifics. To identify baseline performance metrics on the effects of irradiation on the gut microbiome of mass-reared flies in Hawai\'i, a study was performed to assess performance metrics and microbiome (bacterial 16S rRNA) variation across multiple timepoints. Mediterranean fruit fly pupae were selected from mass-reared trays intended for release, and paired samples were either irradiated or remained as controls and transported to the laboratory for evaluation. Irradiated flies exhibited fewer successful fliers, more rapid mortality rates, and were less active relative to control nonirradiated flies. Contrary to initial expectations, irradiation did not exert substantial impacts on the composition or diversity of bacterial reads. Samples were primarily comprised of sequences classified as Klebsiella and there were low levels of both read and taxonomic diversity relative to other 16S surveys of medfly. Although this study does not demonstrate a strong effect of irradiation alone on the Mediterranean fruit fly microbiome, there are several explanations for this discrepancy.