Determination of Lipid Degradation by Marine Lipase-Producing Bacteria: Critical Evaluation of Lipase Activity Assays

Current perspectives for microbial lipases from extremophiles and metagenomics

Microbial lipases are most broadly used biocatalysts for environmental and industrial applications. Lipases catalyze the hydrolysis and synthesis of long acyl chain esters and have a characteristic folding pattern of α/β hydrolase with highly conserved catalytic triad (Serine, Aspartic/Glutamic acid and Histidine). Mesophilic lipases (optimal activity in neutral pH range, mesophilic temperature range, atmospheric pressure, normal salinity, non-radio-resistant, and instability in organic solvents) have been in use for many industrial biotransformation reactions. However, lipases from extremophiles can be used to design biotransformation reactions with higher yields, less byproducts or useful side products and have been predicted to catalyze those reactions also, which otherwise are not possible with the mesophilic lipases. The extremophile lipase perform activity at extremes of temperature, pH, salinity, and pressure which can be screened from metagenome and de novo lipase design using computational approaches. Despite structural similarity, they exhibit great diversity at the sequence level. This diversity is broader when lipases from the bacterial, archaeal, plant, and animal domains/kingdoms are compared. Furthermore, a great diversity of novel lipases exists and can be discovered from the analysis of the dark matter - the unexplored nucleotide/metagenomic databases. This review is an update on extremophilic microbial lipases, their diversity, structure, and classification. An overview on novel lipases which have been detected through analysis of the genomic dark matter (metagenome) has also been presented.

Identification of new members of alkaliphilic lipases in archaea and metagenome database using reconstruction of ancestral sequences

The application of bioinformatics in lipase research has the potential to discover robust members from different genomic/metagenomic databses. In this study, we explored the diversity and distribution of alkaliphilic lipases in archaea domain and metagenome data sets through phylogenetic survey. Reconstructed ancestral sequence of alkaphilic lipase was used to search the homologous alkaliphilic lipases among the archaea and metagenome public databases. Our investigation revealed a total 21 unique sequences of new alkaliphilic lipases in the archaeal and environmental metagenomic protein databases that shared significant sequence similarity to the bacterial alkaliphilic lipases. Most of the identified new members of alkaliphilic lipases belong to class Haloarchaea. The searched list of homologs also comprised of one characterized lipase from alkalohyperthermophilic Archaeoglobus fulgidus. All the newly identified alkaliphilic lipase members showed conserved pentapeptide [X-His-Ser-X-Gly] motif, a key feature of lipase family. Furthermore, detailed analysis of all these new sequences showed homology either with thermostable or alkalophilic lipases. The reconstructed ancestral sequence-based searches increased the sensitivity and efficacies to detect remotely homologous sequences. We hypothesize that this study can enrich our current knowledge on lipases in designing more potential thermo-alkaliphilic lipases for industrial applications.

Microbial Surface Colonization and Biofilm Development in Marine Environments

Biotic and abiotic surfaces in marine waters are rapidly colonized by microorganisms. Surface colonization and subsequent biofilm formation and development provide numerous advantages to these organisms and support critical ecological and biogeochemical functions in the changing marine environment. Microbial surface association also contributes to deleterious effects such as biofouling, biocorrosion, and the persistence and transmission of harmful or pathogenic microorganisms and their genetic determinants. The processes and mechanisms of colonization as well as key players among the surface-associated microbiota have been studied for several decades. Accumulating evidence indicates that specific cell-surface, cell-cell, and interpopulation interactions shape the composition, structure, spatiotemporal dynamics, and functions of surface-associated microbial communities. Several key microbial processes and mechanisms, including (i) surface, population, and community sensing and signaling, (ii) intraspecies and interspecies communication and interaction, and (iii) the regulatory balance between cooperation and competition, have been identified as critical for the microbial surface association lifestyle. In this review, recent progress in the study of marine microbial surface colonization and biofilm development is synthesized and discussed. Major gaps in our knowledge remain. We pose questions for targeted investigation of surface-specific community-level microbial features, answers to which would advance our understanding of surface-associated microbial community ecology and the biogeochemical functions of these communities at levels from molecular mechanistic details through systems biological integration.

Microbial Control of Sea Spray Aerosol Composition: A Tale of Two Blooms

With the oceans covering 71% of the Earth, sea spray aerosol (SSA) particles profoundly impact climate through their ability to scatter solar radiation and serve as seeds for cloud formation. The climate properties can change when sea salt particles become mixed with insoluble organic material formed in ocean regions with phytoplankton blooms. Currently, the extent to which SSA chemical composition and climate properties are altered by biological processes in the ocean is uncertain. To better understand the factors controlling SSA composition, we carried out a mesocosm study in an isolated ocean-atmosphere facility containing 3,400 gallons of natural seawater. Over the course of the study, two successive phytoplankton blooms resulted in SSA with vastly different composition and properties. During the first bloom, aliphatic-rich organics were enhanced in submicron SSA and tracked the abundance of phytoplankton as indicated by chlorophyll-a concentrations. In contrast, the second bloom showed no enhancement of organic species in submicron particles. A concurrent increase in ice nucleating SSA particles was also observed only during the first bloom. Analysis of the temporal variability in the concentration of aliphatic-rich organic species, using a kinetic model, suggests that the observed enhancement in SSA organic content is set by a delicate balance between the rate of phytoplankton primary production of labile lipids and enzymatic induced degradation. This study establishes a mechanistic framework indicating that biological processes in the ocean and SSA chemical composition are coupled not simply by ocean chlorophyll-a concentrations, but are modulated by microbial degradation processes. This work provides unique insight into the biological, chemical, and physical processes that control SSA chemical composition, that when properly accounted for may explain the observed differences in SSA composition between field studies.