Biology subjects

Wilbanks, E. G.

Publications and source records attributed to Wilbanks, E. G..

4 recordsLinked to original sources

bioRxiv2025

Multiscale mechanics of granular biofilms

Biofilms produce and maintain extracellular polymeric substances (EPS) essential for their form and function. While biofilms are commonly lamellar and frequently targets of removal, granular biofilms are increasingly incorporated into water treatment strategies. In both cases, the EPS (mainly consisting of proteins, polysaccharides, and extracellular DNA) is largely responsible for their persistence. Unlike many granular biofilms, which are formed in engineered industrial bioreactors, the "pink berry" consortia is a naturally-occurring and robust granular biofilm of photosynthetic bacteria, found only in intertidal pools of salt marshes around Woods Hole, Massachusetts (USA). The pink berry biofilms unique ecological niche has sparked over three decades of study, yet their mechanical properties are completely unknown. Here, we characterized the structural and mechanical landscape of pink berry granules to determine the extent to which microscale heterogeneity influences macroscale material properties. We performed microindentation measurements on intact granules and nanoindentation measurements on thin sections. We report that intact pink berry granules exhibited low reduced elastic moduli (E*pink berry {approx} 0.5-10 kPa) and fast stress relaxation times ({tau}1/2 {approx} seconds), consistent with previous investigations of soft and viscoelastic biofilms. Nanomechanical measurements of thin pink berry sections revealed two mechanically-distinct domains: a very soft extracellular polymeric substance (EPS) matrix surrounding stiffer microcolonies of purple sulfur bacteria (PSB). Light sheet fluorescence microscopy revealed the spatial organization and distribution of cell-dense PSB microcolonies (34 vol.%) within EPS matrix (66 vol.%), suggesting the nanomechanical behavior of EPS dominates macroscale pink berry mechanics. Our multiscale experimental approach combining mechanics and imaging may be broadly applicable to investigations of complex soft materials, from synthetic hydrogel composites to biologically heterogeneous spheroids, organoids, and tissues.

biophysics↗

bioRxiv2024

Maturing giant kelp develop depth-specific microbiomes

Giant kelp (Macrocystis pyrifera) is a photosynthetic macroalga that produces dissolved organic carbon (DOC), essential for marine bacteria and food webs. The bacterial communities residing on giant kelp blades consume and compete for complex carbohydrates, contributing to the microbiome community structure. In this study, we investigate how the microbiome changes in response to the age and depth of giant kelp blades and assess how these changes relate to differences in the hosts photophysiology. We find that the microbial community increases in richness and evenness as kelp blades age. While the microbiomes of juvenile blades are stochastic, communities on mature blades coalesce into less variable, depth-specific community types. Differentially abundant genera in mature microbiomes include members of Bacteroidia and Gammaproteobacteria, known for carbohydrate degradation, and Planctomycetes, which often produce protective secondary metabolites. These shifts in microbiome communities are associated with increased maximum quantum yield of photosystem II of mature blades; therefore, they may be linked to enhanced DOC exudation. By shedding light on these dynamics, our study contributes to a better understanding of the complex interplay between macroalgae, their respective microbiomes, and the surrounding marine environment.

microbiology↗

bioRxiv2023

Targeted hypermutation of putative antigen sensors in multicellular bacteria

Diversity-generating retroelements (DGRs) are used by bacteria, archaea and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these targeted genes. However, the function and benefits of DGR-diversified proteins in cellular hosts remains elusive. We find that 85% of DGRs from one of the major monophyletic lineages of DGR reverse transcriptases are encoded by multicellular bacteria, which often have two or more DGR loci in their genomes. Using the multicellular purple sulfur bacterium Thiohalocapsa sp. PB-PSB1 as an example, we characterized nine distinct DGR loci that cumulatively lead to more than 10294 possible different combinations of target polypeptides. With environmental metagenomes from individual Thiohalocapsa aggregates, we show that most of PB-PSB1s DGR targets are diversified across its biogeographic range, with spatial heterogeneity in the diversity of each locus. In PSB1 and other members of this lineage of cellular DGRs, diversified target genes are associated with NACHT-domain anti-phage defenses and putative ternary conflict systems previously shown to be enriched in multicellular bacteria. We propose that these DGR-diversified target genes act as antigen sensors that confer a form of adaptive immunity to their multicellular consortia. These findings have implications for the emergence of multicellularity, as the NACHT-domain anti-phage systems and ternary systems share both domain homology and conceptual similarities with the innate immune and programmed cell death pathways of plants and metazoans. SignificanceTo defend themselves against predators, bacteria employ a wide range of conflict systems, some of which are enriched in multicellular bacteria. Here, we show that numerous multicellular bacteria use related diversity-generating retroelements (DGRs) to diversify such conflict systems. Error-prone reverse transcription in DGRs introduces random, targeted mutations and rapid diversification. We used Thiohalocapsa PB-PSB1, a member of multicellular bacterial consortia, as a model to study this association between conflict systems and DGRs. We characterized the natural diversity of PB-PSB1 DGRs and propose they function as hypervariable antigen sensors. The accumulation of such DGR-diversified defense systems in multicellular bacteria emphasizes the fitness advantage of a rapidly diversifying immune system for the evolution of multicellularity.

microbiology↗

bioRxiv2021

Metagenomic methylation patterns resolve complex microbial genomes

The plasticity of bacterial and archaeal genomes makes examining their ecological and evolutionary dynamics both exciting and challenging. The same mechanisms that enable rapid genomic change and adaptation confound current approaches for recovering complete genomes from metagenomes. Here, we use strain-specific patterns of DNA methylation to resolve complex bacterial genomes from the long-read metagenome of a marine microbial consortia, the "pink berries" of the Sippewissett Marsh. Unique combinations of restriction-modification (RM) systems encoded by the bacteria produced distinctive methylation profiles that accurately binned and classified metagenomic sequences. We linked the methylation patterns of each metagenome-assembled genome with encoded DNA methyltransferases and discovered new restriction modification (RM) defense systems, including novel associations of RM systems with RNase toxins. Using this approach, we finished the largest and most complex circularized bacterial genome ever recovered from a metagenome (7.9 Mb with >600 IS elements), the finished genome of Thiohalocapsa sp. PB-PSB1 the dominant bacteria in the consortia. From these methylation-binned genomes, we identified instances of lateral gene transfer between sulfur-cycling symbionts (Thiohalocapsa sp. PB-PSB1 and Desulfofustis sp. PB-SRB1), phage infection, and strain-level structural variation.

microbiology↗