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A Gram-stain-negative, long-rod-shaped and facultative aerobic bacterium, designated HB-1T, was isolated from a round hay bale at the Kansas State University Beef Stocker Unit. The results of phylogenetic analysis of 16S rRNA gene sequences indicated that strain HB-1T clustered within the genus Gemmobacter and its closest relatives were Gemmobacter aquaticus A1-9T (98.0 %), Gemmobacter lutimaris YJ-T1-11T (98.0 %), Gemmobacter fontiphilus JS43T (97.8 %), Gemmobacter aquatilis DSM 3857T (97.5 %) and Gemmobacter lanyuensis Orc-4T (96.9 %). Additional phylogenomic analysis also indicated that strain HB-1T belongs to the genus Gemmobacter . The draft genome of strain HB-1T had a total length of 4.23 Mbp and contained 4071 protein-coding genes. The average nucleotide identity values between the genomes of strain HB-1T and the three most-related type strains ranged from 77.5 to 78.1 %. The DNA G+C content of strain HB-1T was 63.7 mol%. The novel strain grew at 10–37 °C, pH 5–10 and with 0–2 % NaCl. Oxidase and catalase activities were positive. Cells were 0.3–0.4 µm wide, 3.0–7.0 µm long and usually found in pairs or chains of cells. The major respiratory quinone of strain HB-1T was Q-10 (90 %), with a minor amount of Q-9 (10 %). The major fatty acids were C18 : 1  ω7c (54.6 %) and C16 : 0 (18.2 %). On the basis of phenotypic, phylogenetic and chemotaxonomic data, strain HB-1T (=DSM 109828T=ATCC TSD-211T) is considered to represent a novel species of the genus Gemmobacter , for which the name Gemmobacter serpentinus sp. nov. is proposed.

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Multispecies biofilms are a common limitation in membrane bioreactors, causing membrane clogging, degradation, and failure. There is a poor understanding of biological fouling mechanisms in these systems due to the limited number of experimental techniques useful for probing microbial interactions at the membrane interface. Here, we develop a new experimental method, termed polymer surface dissection (PSD), to investigate multispecies assembly processes over membrane surfaces. The PSD method uses photodegradable polyethylene glycol hydrogels functionalized with bioaffinity ligands to bind and detach microscale, microbial aggregates from the membrane for microscopic observation. Subsequent exposure of the hydrogel to high resolution, patterned UV light allows for controlled release of any selected aggregate of desired size at high purity for DNA extraction. Follow-up 16S community analysis reveals aggregate composition, correlating microscopic images with the bacterial community structure. The optimized approach can isolate aggregates with microscale spatial precision and yields genomic DNA at sufficient quantity and quality for sequencing from aggregates with areas as low as 2000 μm2, without the need of culturing for sample enrichment. To demonstrate the value of the approach, PSD was used to reveal the composition of microscale aggregates of different sizes during early-stage biofouling of aerobic wastewater communities over PVDF membranes. Larger aggregates exhibited lower diversity of bacterial communities, and a shift in the community structure was found as aggregate size increased to areas between 25,000 and 45,000 μm2, below which aggregates were more enriched in Bacteroidetes and above which aggregates were more enriched with Proteobacteria. The findings demonstrate that community succession can be observed within microscale aggregates and that the PSD method is useful for identification and characterization of early colonizing bacteria that drive biofouling on membrane surfaces.

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