Coordinated proteome change precedes cell lysis and death in a mat-forming cyanobacterium

Cyanobacteria form dense multicellular communities that experience transient conditions in terms of access to light and oxygen. These systems are productive but also undergo substantial biomass turnover through cell death, supplementing heightened heterotrophic respiration. Here we use metagenomics and metaproteomics to survey the molecular response of a mat-forming cyanobacterium undergoing mass cell lysis after exposure to dark and anoxic conditions. A lack of evidence for viral, bacterial, or eukaryotic antagonism contradicts commonly held beliefs on the causative agent for cyanobacterial death during dense growth. Instead, proteogenomics data indicated that lysis likely resulted from a genetically programmed response triggered by a failure to maintain osmotic pressure in the wake of severe energy limitation. Cyanobacterial DNA was rapidly degraded, yet cyanobacterial proteins remained abundant. A subset of proteins, including enzymes involved in amino acid metabolism, peptidases, toxin-antitoxin systems, and a potentially self-targeting CRISPR-Cas system, were upregulated upon lysis, indicating possible involvement in the programmed cell death response. We propose this natural form of cell death could provide new pathways for controlling harmful algal blooms and for sustainable bioproduct production.

SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis

Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most of the work is performed far away from sample collection in both space and time. Performing amplicon sequencing and analysis at sample collection would have positive implications in many instances including remote fieldwork and point-of-care medical diagnoses. Here we present SituSeq, an offline and portable workflow for the sequencing and analysis of 16S rRNA gene amplicons using Nanopore sequencing and a standard laptop computer. SituSeq was validated by comparing Nanopore 16S rRNA gene amplicons, Illumina 16S rRNA gene amplicons, and Illumina metagenomes, sequenced using the same environmental DNA. Comparisons revealed consistent community composition, ecological trends, and sequence identity across platforms. Correlation between the abundance of taxa in each taxonomic level in Illumina and Nanopore data sets was high (Pearson's r > 0.9), and over 70% of Illumina 16S rRNA gene sequences matched a Nanopore sequence with greater than 97% sequence identity. On board a research vessel on the open ocean, SituSeq was used to analyze amplicon sequences from deep sea sediments less than 2 h after sequencing, and 8 h after sample collection. The rapidly available results informed decisions about subsequent sampling in near real-time while the offshore expedition was still underway. SituSeq is a portable and user-friendly workflow that helps to bring the power of microbial genomics and diagnostics to many more researchers and situations.

Seasonal bacterial niche structures and chemolithoautotrophic ecotypes in a North Atlantic fjord

Quantifying the temporal change of bacterial communities is essential to understanding how both natural and anthropogenic pressures impact the functions of coastal marine ecosystems. Here we use weekly microbial DNA sampling across four years to show that bacterial phyla have distinct seasonal niches, with a richness peak in winter (i.e., an inverse relationship with daylength). Our results suggest that seasonal fluctuations, rather than the kinetic energy or resource hypotheses, dominated the pattern of bacterial diversity. These findings supplement those from global analyses which lack temporal replication and present few data from winter months in polar and temperate regions. Centered log-ratio transformed data provided new insights into the seasonal niche partitioning of conditionally rare phyla, such as Modulibacteria, Verrucomicrobiota, Synergistota, Deinococcota, and Fermentibacterota. These patterns could not be identified using the standard practice of ASV generation followed by rarefaction. Our study provides evidence that five globally relevant ecotypes of chemolithoautotrophic bacteria from the SUP05 lineage comprise a significant functional group with varying seasonal dominance patterns in the Bedford Basin.

Geological processes mediate a microbial dispersal loop in the deep biosphere

The deep biosphere is the largest microbial habitat on Earth and features abundant bacterial endospores. Whereas dormancy and survival at theoretical energy minima are hallmarks of microbial physiology in the subsurface, ecological processes such as dispersal and selection in the deep biosphere remain poorly understood. We investigated the biogeography of dispersing bacteria in the deep sea where upward hydrocarbon seepage was confirmed by acoustic imagery and geochemistry. Thermophilic endospores in the permanently cold seabed correlated with underlying seep conduits reveal geofluid-facilitated cell migration pathways originating in deep petroleum-bearing sediments. Endospore genomes highlight adaptations to life in anoxic petroleum systems and bear close resemblance to oil reservoir microbiomes globally. Upon transport out of the subsurface, viable thermophilic endospores reenter the geosphere by sediment burial, enabling germination and environmental selection at depth where new petroleum systems establish. This microbial dispersal loop circulates living biomass in and out of the deep biosphere.

CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation

Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation.

The Effect of Dissimilatory Manganese Reduction on Lactate Fermentation and Microbial Community Assembly

Fermentation and dissimilatory manganese (Mn) reduction are inter-related metabolic processes that microbes can perform in anoxic environments. Fermentation is less energetically favorable and is often not considered to compete for organic carbon with dissimilatory metal reduction. Therefore, the aim of our study was to investigate the outcome of the competition for lactate between fermentation and Mn oxide (birnessite) reduction in a mixed microbial community. A birnessite reducing enrichment culture was obtained from activated sludge with lactate and birnessite as the substrates. This enrichment was further used to test how various birnessite activities (0, 10, 20, and 40 mM) affected the rates of fermentation and metal reduction, as well as community composition. Increased birnessite activity led to a decrease of lactate consumption rate. Acetate and propionate were the main products. With increasing birnessite activity, the propionate/acetate ratio decreased from 1.4 to 0.47. Significant CO₂ production was detected only in the absence of birnessite. In its presence, CO₂ concentrations remained close to the background since most of the CO₂ produced in these experiments was recovered as MnCO₃. The Mn reduction efficiency (Mn(II) produced divided by birnessite added) was the highest at 10 mM birnessite added, where about 50% of added birnessite was reduced to Mn(II), whereas at 20 and 40 mM approximately 21 and 16% was reduced. The decreased birnessite reduction efficiency at higher birnessite activities points to inhibition by terminal electron acceptors and/or its toxicity which was also indicated by retarded lactate oxidation and decreased concentrations of microbial metabolites. Birnessite activity strongly affected microbial community structure. Firmicutes and Bacteroidetes were the most abundant phyla at 0 mM of birnessite. Their abundance was inversely correlated with birnessite concentration. The relative sequence abundance of Proteobacteria correlated with birnessite concentrations. Most of the enriched populations were involved in lactate/acetate or amino acid fermentation and the only previously known metal reducing genus detected was related to Shewanella sp. The sequencing data confirmed that lactate consumption coupled to metal reduction was only one of the processes occurring and did not outcompete fermentation processes.

Drivers of Regional Bacterial Community Structure and Diversity in the Northwest Atlantic Ocean

The fundamental role of bacteria in global biogeochemical cycles warrants a thorough understanding of the factors controlling bacterial community structure. In this study, the integrated effect of seasonal differences and spatial distribution on bacterial community structure and diversity were investigated at the regional scale. We conducted a comprehensive bacterial survey, with 451 samples of the Scotian Shelf sector of the Northwest Atlantic Ocean during spring and fall of 2014 and 2016, to analyze the effects of physicochemical gradients on bacterial community structure. Throughout the region, Pelagibacteraceae and Rhodobacteraceae were the most common in the free-living fraction, while Flavobacteriia and Deltaproteobacteria were more abundant in the particle-associated fraction. Overall, there was strong covariation of the microbial community diversity from the two size fractions. This relationship existed despite the statistically significant difference in community structure between the free-living and particle-associated size fractions. In both size fractions, distribution patterns of bacterial taxa, and species within taxa, displayed temporal and spatial preferences. Distinct bacterial assemblages specific to season and depth in the water column were identified. These distinct assemblages, consistent for both 2014 and 2016, suggested replicable patterns in microbial communities for spring and fall in this region. Over all sites, temperature and oxygen values were highly correlated with community similarity, and salinity and oxygen values were the most strongly positively- and negatively correlated with alpha diversity, respectively. However, the strengths of these correlations depended on the depth and season sampled. The bathymetry of the Scotian Shelf, the abrupt shelf break to the Scotian Slope and the major ocean currents dominating in the region led to the formation of distinct on-shelf and off-shelf bacterial communities both in spring and fall. The highest species richness was observed at the shelf break, where water masses from the two major currents meet. Our study establishes the baseline for assessing future changes in the bacterial community of the Scotian Shelf waters, a rapidly changing sector of the Atlantic Ocean.