Graphical abstract

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.

Alkaline soda lakes are known as some of nature’s most biologically productive ecosystems. Vigorous production (photosynthetic conversion of inorganic carbon into biomass) is countered by incremental biomass degradation, which fuels and feeds a diverse microbial community. Learn here about key adaptations that help microbes survive and thrive in the extreme conditions of alkaline soda lakes. Dive into the interconnected microbial element cycles of alkaline soda lakes and discover how the geochemistry of these environments presents microbes with unique challenges and opportunities. Throughout this article, explore how the microbial inhabitants of alkaline soda lakes have been harnessed in biotechnological applications, including the production of protein-rich food, detergent enzymes, and the purification of biogas.

In many industries, from food to biofuels, contamination of production systems with predators is a costly problem and requires the maintenance of sterile operating conditions. In this study, we look at the robustness of one such alkaliphilic consortium, comprised largely of a cyanobacteriumCandidatusPhormidium alkaliphilum, to viral predation. This consortium has existed without a community crash over several years in laboratory and pilot scale environments. We look at CRISPR-Cas systems and viral dynamics in this consortium at four conditions using metagenomic analyses. Results show that while there are active viral members in this community, viral predation of the cyanobacteria is low and does not affect the community dynamics. The multiple CRISPR arrays within the Phormidium were found to be static following initial lab establishment of consortium. Multiple cryptic CRISPR-Cas systems were detected with uncertain viral protection capacity. Our results suggest that dynamics of potential viruses and CRISPR-Cas mediated immunity likely play an important role in the initial establishment of consortia and may continue to support the functional robustness of engineered microbial communities throughout biotechnology applications.ImportanceBiotechnology applications utilizing the function of microbial communities have become increasingly important solutions as we strive for sustainable applications. Although viral infections are known to have significant impact on microbial turnover and nutrient cycling, viral dynamics have remained largely overlooked in these engineered communities. Predatory perturbations to the functional stability of these microbial biotechnology applications must be investigated in order to design more robust applications. In this study, we closely examine virus-microbe dynamics in a model microbial community used in a biotechnology application. Our findings suggest that viral dynamics change significantly with environmental conditions and that microbial immunity may play an important role in maintaining functional stability. We present this study as a comprehensive template for other researchers interested in exploring predatory dynamics in engineered microbial communities.