Metagenomic Analysis of the Gut Microbiome of the Common Black Slug Arion ater in Search of Novel Lignocellulose Degrading Enzymes

Abstract

Some eukaryotes are able to gain access to well-protected carbon sources in plant biomass by exploiting microorganisms in the environment or harbored in their digestive system. One is the land pulmonate Arion ater, which takes advantage of a gut microbial consortium that can break down the widely available, but difficult to digest, carbohydrate polymers in lignocellulose, enabling them to digest a broad range of fresh and partially degraded plant material efficiently. This ability is considered one of the major factors that have enabled A. ater to become one of the most widespread plant pest species in Western Europe and North America. Using metagenomic techniques we have characterized the bacterial diversity and functional capability of the gut microbiome of this notorious agricultural pest. Analysis of gut metagenomic community sequences identified abundant populations of known lignocellulose-degrading bacteria, along with well-characterized bacterial plant pathogens. This also revealed a repertoire of more than 3,383 carbohydrate active enzymes (CAZymes) including multiple enzymes associated with lignin degradation, demonstrating a microbial consortium capable of degradation of all components of lignocellulose. This would allow A. ater to make extensive use of plant biomass as a source of nutrients through exploitation of the enzymatic capabilities of the gut microbial consortia. From this metagenome assembly we also demonstrate the successful amplification of multiple predicted gene sequences from metagenomic DNA subjected to whole genome amplification and expression of functional proteins, facilitating the low cost acquisition and biochemical testing of the many thousands of novel genes identified in metagenomics studies. These findings demonstrate the importance of studying Gastropod microbial communities. Firstly, with respect to understanding links between feeding and evolutionary success and, secondly, as sources of novel enzymes with biotechnological potential, such as, CAZYmes that could be used in the production of biofuel.

Compositional and predicted functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing

“…Previous studies with the snail A. fulica showed that many particular functional genes in the gut microbiota (e.g., genes associated with the production of amino acids, fatty acids, cofactors, vitamins, and enzymes) are required by the hosts for plant fiber degradation ( Cardoso et al, 2012a ). As recently reported by Joynson et al (2017) , 2,510 genes corresponding to glycoside hydrolase activity and 561 carbohydrate-binding modules were identified in a total of 108,691 putative genes of the gut microbiome of the common black slug Arion ater . The microbiotic function predicted in our study are also necessary for many physiological functions.…”

Deconstruction of Lignin: From Enzymes to Microorganisms

“…A repertoire of lignocellulose-degrading enzymes has also been identified in the gut microbiome of the common black slug Arion. This study revealed more than 3383 CAZymes including multiple AAs families, associated with lignin degradation including members of the AA2, AA3, and AA4 families, which are involved in oxidative degradation, and the AA6 family, which catalyze the biodegradation of aromatic compounds such as monolignols [ 73 ].…”

Environment and Diet Influence the Bacterial Microbiome of Ambigolimax valentianus, an Invasive Slug in California

“…Determining the extent of bacterial genes associated with lignocellulose degradation in A. valentianus could be economically significant and relevant for food security. The diversity of the core bacterial microbiome of A. valentianus slugs in this study is slightly more diverse than slug microbiomes analyzed in previous studies [15,17,85]. This could be due to our use of whole slugs in this study, whereas other studies limited their microbiome analyses to specific regions of the slug's anatomy [15,17,85].…”

“…The variations in the structure of the bacterial microbiome of A. valentianus could be attributed to a range of factors. Nonetheless, this research, as well as many other snail and slug studies, has demonstrated that Proteobacteria are the dominant species found among these gastropod microbiomes, regardless of feeding conditions or nutrient uptake (sterile diet, starved, complete diet) [12][13][14][15][16][17][18][19][20][21][22][23][24][25][26]. Further investigation into the nutritional and digestive roles of the bacterial microbiome of A. valentianus would provide more insight into the specificity of their associated bacteria.…”