Red calcified non-geniculate coralline algae (NGCA) provide habitat structures, stabilize reef structures, and foster coral larval settlement and metamorphosis. Moreover, the microbes associated with NGCA are dependent on the NGCA host species and are affected by environmental factors; however, little is known about the influence of reef conditions and depth gradients on the associated microbial communities and NGCA. In this study, we collected NGCA under different reef conditions and depth gradients and characterized the microbial communities using the V3-V4 hypervariable regions of the 16S rRNA gene. Metagenomic analysis revealed 2 domains, 51 phyla, 123 classes, and 210 genera. The NGCA-associated bacterial communities were dominated by Proteobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, and Acidobacteriota. Gammaproteobacteria and Alphaproteobacteria were the most abundant bacterial classes. Differences in microbial diversity and richness were not apparent between reef conditions and depth gradients. However, there was a significant difference in bacterial evenness among the depth gradients. The bacterial abundance associated with NGCA was greater in deep zones than in shallow zones. The shallow zone exhibited a greater relative abundance of all gene functions than the deep zone, indicating differences in the distribution of gene functions. This study showed that the microbial communities associated with red calcified NGCA are diverse, and that the depth gradient affects their abundance and evenness, highlighting the need for further research to understand the functional roles of these microbial communities in coral reef conservation.

The increasing threats to ecosystems and humans from marine plastic pollution require a comprehensive assessment. We present a plastisphere case study from Reunion Island, a remote oceanic island located in the Southwest Indian Ocean, polluted by plastics. We characterized the plastic pollution on the island\'s coastal waters, described the associated microbiome, explored viable bacterial flora and the presence of antimicrobial resistant (AMR) bacteria. Reunion Island faces plastic pollution with up to 10,000 items/km2 in coastal water. These plastics host microbiomes dominated by Proteobacteria (80 %), including dominant genera such as Psychrobacter, Photobacterium, Pseudoalteromonas and Vibrio. Culturable microbiomes reach 107 CFU/g of microplastics, with dominance of Exiguobacterium and Pseudomonas. Plastics also carry AMR bacteria including β-lactam resistance. Thus, Southwest Indian Ocean islands are facing serious plastic pollution. This pollution requires vigilant monitoring as it harbors a plastisphere including AMR, that threatens pristine ecosystems and potentially human health through the marine food chain.

Free-living and symbiotic chemosynthetic microbial communities support primary production and higher trophic levels in deep-sea hydrothermal vents. The shrimp Rimicaris exoculata, which dominates animal communities along the Mid-Atlantic Ridge, houses a complex bacterial community in its enlarged cephalothorax. The dominant bacteria present are from the taxonomic groups Campylobacteria, Desulfobulbia (formerly Deltaproteobacteria), Alphaproteobacteria, Gammaproteobacteria, and some recently discovered iron oxyhydroxide-coated Zetaproteobacteria. This epibiotic consortium uses iron, sulfide, methane, and hydrogen as energy sources. Here, we generated shotgun metagenomes from Rimicaris exoculata cephalothoracic epibiotic communities to reconstruct and investigate symbiotic genomes. We collected specimens from three geochemically contrasted vent fields, TAG, Rainbow, and Snake Pit, to unravel the specificity, variability, and adaptation of Rimicaris-microbe associations.
Our data enabled us to reconstruct 49 metagenome-assembled genomes (MAGs) from the TAG and Rainbow vent fields, including 16 with more than 90% completion and less than 5% contamination based on single copy core genes. These MAGs belonged to the dominant Campylobacteria, Desulfobulbia, Thiotrichaceae, and some novel candidate phyla radiation (CPR) lineages. In addition, most importantly, two MAGs in our collection were affiliated to Zetaproteobacteria and had no close relatives (average nucleotide identity ANI < 77% with the closest relative Ghiorsea bivora isolated from TAG, and 88% with each other), suggesting potential novel species. Genes for Calvin-Benson Bassham (CBB) carbon fixation, iron, and sulfur oxidation, as well as nitrate reduction, occurred in both MAGs. However, genes for hydrogen oxidation and multicopper oxidases occurred in one MAG only, suggesting shared and specific potential functions for these two novel Zetaproteobacteria symbiotic lineages. Overall, we observed highly similar symbionts co-existing in a single shrimp at both the basaltic TAG and ultramafic Rainbow vent sites. Nevertheless, further examination of the seeming functional redundancy among these epibionts revealed important differences.
These data highlight microniche partitioning in the Rimicaris holobiont and support recent studies showing that functional diversity enables multiple symbiont strains to coexist in animals colonizing hydrothermal vents. Video Abstract.

In recent years, the microbiome field has undergone a shift from clustering-based methods of operational taxonomic unit (OTU) designation based on sequence similarity to denoising algorithms that identify exact amplicon sequence variants (ASVs), and methods to identify contaminating bacterial DNA sequences from low biomass samples have been developed. Although these methods improve accuracy when analyzing mock communities, their impact on real samples and downstream analysis of biological associations is less clear.
Here, we re-processed our recently published milk microbiota data using Qiime1 to identify OTUs, and Qiime2 to identify ASVs, with or without contaminant removal using decontam. Qiime2 resolved the mock community more accurately, primarily because Qiime1 failed to detect Lactobacillus. Qiime2 also considerably reduced the average number of ASVs detected in human milk samples (364 ± 145 OTUs vs. 170 ± 73 ASVs, p < 0.001). Compared to the richness, the estimated diversity measures had a similar range using both methods albeit statistically different (inverse Simpson index: 14.3 ± 8.5 vs. 15.6 ± 8.7, p = 0.031) and there was strong consistency and agreement for the relative abundances of the most abundant bacterial taxa, including Staphylococcaceae and Streptococcaceae. One notable exception was Oxalobacteriaceae, which was overrepresented using Qiime1 regardless of contaminant removal. Downstream statistical analyses were not impacted by the choice of algorithm in terms of the direction, strength, and significance of associations of host factors with bacterial diversity and overall community composition.
Overall, the biological observations and conclusions were robust to the choice of the sequencing processing methods and contaminant removal.

To better understand the characteristics of soil bacterial diversity in different environments, the Laiwu Qilongwan experimental site was selected as it is of great significance for the study of geochemical cycles. The soil CO2, mineral composition and bacterial community were analyzed by an EGM-4 portable environmental gas detector, an X-ray diffractometer and 16S rDNA high-throughput sequencing, and soil bacterial diversity and the relationship between soil bacterial diversity and environmental factors were studied. The results showed that with increasing soil depth, the CO2 content increased, the feldspar and amphibole contents increased, the quartz content decreased, the richness of the soil bacterial community increased, the relative richness of Nitrospirae increased, and Chloroflexi decreased. The dominant bacteria were Proteobacteria, Actinobacteria and Acidobacteria. There were slight differences in soil CO2, mineral composition and dominant bacterial flora at the same depth. Actinobacteria, Proteobacteria and Firmicutes were the dominant phyla of L02. The CO2 was lowest in bare land, and the quartz and K-feldspar contents were the highest. Soil CO2 mainly affected the deep bacterial diversity, while shallow soil bacteria were mainly affected by mineral components (quartz and K-feldspar). At the same depth, amphibole and clay minerals had obvious effects on the bacterial community, while CO2 had obvious effects on subdominant bacteria.

The microbial communities residing in the child gut are thought to play an important role in child growth, although the relationship is not well understood. We examined a cohort of young children from Mirzapur, Bangladesh, prospectively over 18 months. Four fecal markers of environmental enteropathy (EE) (high levels of alpha-1-antitrypsin, calprotectin, myeloperoxidase, and neopterin) were examined and anthropometric measures obtained from a cohort of 68 children. The 16S rRNA gene of bacterial DNA was sequenced from stool samples and used to estimate amplicon sequence variants (ASVs). We age-matched children with poor growth to children with normal growth within 1 month and compared the change in abundance and diversity of ASVs over time. Elevated EE markers and poor linear growth in children were associated with changes in microbial communities in the gut. There were increased amounts of Escherichia/Shigella and Proteobacteria and decreased amounts of Prevotella associated with poorly growing children consistent with the mounting evidence supporting the relationship between intestinal inflammation, child growth, and changes in gut microbiota composition. Future research is needed to investigate this association among young children in low- and middle-income countries.

The present work aimed to design a degenerate primer pair to target a large part of the hppd soil bacterial community, possibly affected by herbicides. We validated these primers by qPCR and high-throughput sequencing analysis of soil samples.

BACKGROUND: The presentation of sepsis and bacteremia in cutaneous and cavitary myiasis is uncommon. We present a patient, residing in a temperate region of the United States, with myiasis and sepsis from the emerging human pathogens Wohlfahrtiimonas chitiniclastica and Ignatzschineria indica.
METHODS: A 37-year-old male patient with an 8-month history of chronic lymphedema and ulcers of the lower left extremity presented with myiasis of the left foot and leg. The patient was initially seen by his family practitioner many times and was prescribed antibiotics which he could not afford. Debridement of the myiasis was not conducted by the family practitioner due to the belief that the patient\'s current state of myiasis would effectively debride and eventually heal the chronic ulcers along with multiple antibiotic regimens. Over the 8-month period, the patient developed a progressive, painful, necrotizing infection of his lower left extremity.
METHODS: Physical examination clearly showed myiasis of the patient\'s lower left extremity, believed to be caused by Lucilia sericata (green bottle fly). Blood cultures revealed the presence of Providencia stuartii, W chitiniclastica, and I indica to be the underlying cause of sepsis and bacteremia.
METHODS: All visible maggots were extracted, debridement of devitalized tissue was performed, and the leg ulcers were wrapped in pH neutral bleach. The patient was initially treated with a broad-spectrum antibiotic regimen of vancomycin, clindamycin, piperacillin, and tazobactam which, following clinical improvement, was de-escalated to cefepime.
RESULTS: The fly larvae and maggots were removed from the extremity by scrubbing, pulse lavage, and filing away the callused tissue. Additionally, the patient\'s sepsis and bacteremia, caused by W chitiniclastica and I indica, were successfully treated through antibiotic intervention. Amputation was avoided.
CONCLUSIONS: The use of pulse lavage and chlorhexidine-soaked brushes for the removal of cavitary myiasis is an effective and minimally invasive procedure which does not cause additional damage to surrounding tissue. W chitiniclastica and I indica are emerging bacteria that have known association to parasitic fly myiasis in humans and are capable of causing sepsis and/or bacteremia if not accurately identified and treated promptly.

Polyacrylamides (PAMs) are used in sand and gravel quarries as water purification flocculants for recycling process water in a recycling loop system where the flocculants remove fine particles in the form of sludge. The PAM-based flocculants, however, contain residual amounts of acrylamide (AMD) that did not react during the polymerization process. This acrylamide is released into the environment when the sludge is discharged into a settling basin. Here, we explore the microbial diversity and the potential for AMD biodegradation in water and sludge samples collected in a quarry site submitted to low AMD concentrations. The microbial diversity, analyzed by culture-dependent methods and the denaturing gradient gel electrophoresis approach, reveals the presence of Proteobacteria, Cyanobacteria, and Actinobacteria, among which some species are known to have an AMD biodegradation activity. Results also show that the two main parts of the water recycling loop-the washing process and the settling basin-display significantly different bacterial profiles. The exposure time with residual AMD could, thus, be one of the parameters that lead to a selection of specific bacterial species. AMD degradation experiments with 0.5 g L(-1) AMD showed a high potential for biodegradation in all parts of the washing process, except the make-up water. The AMD biodegradation potential in samples collected from the washing process and settling basin was also analyzed taking into account on-site conditions: low (12 °C) and high (25 °C) temperatures reflecting the winter and summer seasons, and AMD concentrations of 50 μg L(-1). Batch tests showed rapid (as little as 18 h) AMD biodegradation under aerobic and anaerobic conditions at both the winter and summer temperatures, although there was a greater lag time before activity started with the AMD biodegradation at 12 °C. This study, thus, demonstrates that bacteria present in sludge and water samples exert an in situ and rapid biodegradation of AMD at low concentration, whatever the season, and in both the aerobic and anaerobic parts of the water recycling system.

Painful granulomatous lesions appeared on the face of a 36-year-old man with myelodysplastic syndrome. Skin biopsy revealed chronic inflammatory granuloma. Bacterial cultures of the lesions and blood indicated the same unknown Gram-negative rod bacterium. The 16S ribosomal RNA sequence of the unknown bacterium yielded Phenylobacterium. Thus, we diagnosed cutaneous infectious granuloma caused by Phenylobacterium and myelodysplastic syndrome/refractory cytopenia with multi-lineage dysplasia. After treatment with combined antibacterials that were selected based on the tests for drug sensitivity, the lesions disappeared with only scars remaining and without any signs of relapse after 1 year. This is the first case report of cutaneous infectious granuloma caused by Phenylobacterium.