High-Throughput Sequencing Characterizes Intertidal Meiofaunal Communities in Northern Gulf of Mexico (Dauphin Island and Mobile Bay, Alabama)

Abstract

Meiofauna are important components of food webs and for nutrient exchange between the benthos and water column. Recent studies have focused on these communities in the Gulf of Mexico due to potential impacts of the Deepwater Horizon Oil Spill (DWHOS). In particular, intertidal meiofaunal communities from Mobile Bay and Dauphin Island, Alabama, were previously shown to shift from predominately metazoan taxa prior to DWHOS to a fungal-dominated community after the spill. However, knowledge of variability within these communities remains unknown. Herein, we used Illumina high-throughput amplicon sequencing to examine variation throughout a year for the same locations for which the organismal shift was noted. Sediment samples were collected bi-monthly for a year (July 2011-July 2012) from which the meiofaunal community was examined by sequencing the eukaryotic hypervariable V9 region of the 18S rRNA gene. Results showed that the presence of fungal taxa was limited within these communities, suggesting that previously reported acute impacts of the DWHOS on meiofauna were apparently short term. However, these meiofaunal communities show shifts in proportions of metazoan taxa compared to pre-spill samples. Whether this change is due to prolonged impacts of the spill or variation in community composition is unclear. Taxonomic variation within and between sampled locations throughout the study was observed, suggesting potential yearly variation in communities. Continued sampling over a longer timeframe will provide a more complete understanding of seasonality and variation within these communities. Such a baseline is required to assess future anthropogenic impacts.

How Did the Deepwater Horizon Oil Spill Affect Coastal and Continental Shelf Ecosystems of the Gulf of Mexico?

“…Nematodes were the most abundant taxon before oiling but were greatly reduced in abundance after oiling when fungi became dominant. Brannock et al (2014) sampled the same beaches in 2011 and 2012 with the same molecular techniques and observed that fungi had become rare while nematodes and other animal taxa increased in abundance. Thus, the post-spill dominance of fungi on oiled beaches was short-lived, and a more typical metazoan community was found approximately one year after oiling.…”

Meiofaunal community analysis by high-throughput sequencing: Comparison of extraction, quality filtering, and clustering methods

“…These techniques 52 are extremely time consuming and require expertise to properly identify 53 taxonomic groups. More recently, researchers have incorporated high-54 throughput amplicon sequencing targeting specific gene regions to ex-55 plore meiofauna community composition (Chariton et al, 2010;Creer 56 et al, 2010;Fonseca et al, 2010;Creer and Sinniger, 2012;Bik et al, 57 2012a,b,c; Brannock et al, 2014;Fonseca et al, 2014;Lallias et al, 58 2015). Metabarcoding approaches allow for a more comprehensive ex-59 amination of meiofauna community composition as a whole that is not 60 constrained by taxonomic expertise and handling time.…”

“…Metabarcoding approaches allow for a more comprehensive ex-59 amination of meiofauna community composition as a whole that is not 60 constrained by taxonomic expertise and handling time. To date, the ma-61 jority of meiofauna metabarcoding studies have used Roche 454 Life Sci-62 ence pyrosequencing (Chariton et al, 2010); Creer et al, 2010;Fonseca 63 et al, 2010;Creer and Sinniger, 2012;Bik et al, 2012a,b,c;(Fonseca 64 et al, 2014;Lallias et al, 2015), with the Illumina platform being used (Brannock et al, 2014) Fig. 1.…”

“…1). Choice of these amounts was based on what 171 has been used previously (Bik et al, 2012a;Brannock et al, 2014) (Edgar, 2013) resulted in a majority of raw reads 282 (73%) being discarded due to failure to align; therefore, only the 283 PandaSeq overlapped sequences were used for subsequent steps. Overlapped sequences were subjected to two different approaches of 286 quality-filtering.…”

“…Overlapped sequences were subjected to two different approaches of 286 quality-filtering. The first followed the "quality-through-sequence-287 length-filtering" approach implemented in Brannock et al (2014) and 288 from hereafter will be referred to as the FASTX-Toolkit quality filtering.…”