Assessment of the bacterial community structure in shallow and deep sediments of the Perdido Fold Belt region in the Gulf of Mexico

Abstract

The Mexican region of the Perdido Fold Belt (PFB), in northwestern Gulf of Mexico (GoM), is a geological province with important oil reservoirs that will be subjected to forthcoming oil exploration and extraction activities. To date, little is known about the native microbial communities of this region, and how these change relative to water depth. In this study we assessed the bacterial community structure of surficial sediments by high-throughput sequencing of the 16S rRNA gene at 11 sites in the PFB, along a water column depth gradient from 20 to 3,700 m, including five shallow (20–600 m) and six deep (2,800–3,700 m) samples. The results indicated that OTUs richness and diversity were higher for shallow sites (OTUs = 2,888.2 ± 567.88; H′ = 9.6 ± 0.85) than for deep sites (OTUs = 1,884.7 ± 464.2; H′ = 7.74 ± 1.02). Nonmetric multidimensional scaling (NMDS) ordination revealed that shallow microbial communities grouped separately from deep samples. Additionally, the shallow sites plotted further from each other on the NMDS whereas samples from the deeper sites (abyssal plains) plotted much more closely to each other. These differences were related to depth, redox potential, sulfur concentration, and grain size (lime and clay), based on the environmental variables fitted with the axis of the NMDS ordination. In addition, differential abundance analysis identified 147 OTUs with significant fold changes among the zones (107 from shallow and 40 from deep sites), which constituted 10 to 40% of the total relative abundances of the microbial communities. The most abundant OTUs with significant fold changes in shallow samples corresponded to Kordiimonadales, Rhodospirillales, Desulfobacterales (Desulfococcus), Syntrophobacterales and Nitrospirales (GOUTA 19, BD2-6, LCP-6), whilst Chromatiales, Oceanospirillales (Amphritea, Alcanivorax), Methylococcales, Flavobacteriales, Alteromonadales (Shewanella, ZD0117) and Rhodobacterales were the better represented taxa in deep samples. Several of the OTUs detected in both deep and shallow sites have been previously related to hydrocarbons consumption. Thus, this metabolism seems to be well represented in the studied sites, and it could abate future hydrocarbon contamination in this ecosystem. The results presented herein, along with biological and physicochemical data, constitute an available reference for further monitoring of the bacterial communities in this economically important region in the GoM.

N2 fixation dominates nitrogen cycling in a mangrove fiddler crab holobiont

“…Similarly, although it remains speculative whether fiddler crabs take advantage of N 2 fixers residing on their carapace, the depleted 15 N signatures in their tissues compared to other detritivores crab species from the same site may indicate a nutritional relationship between the fiddler crab host and its microbiota. Additionally, the alpha diversity of the crab biofilm prokaryotic community (Shannon’s H ~ 5.5) was within the lower range of prokaryotic diversity reported in previous studies focusing on sediments 42 , 43 , suggesting the occurrence of selection processes on the crab’s carapace.…”

Metagenomic Profiling and Microbial Metabolic Potential of Perdido Fold Belt (NW) and Campeche Knolls (SE) in the Gulf of Mexico

“…However, we are aware that D18 sample is not enough to characterize a complete region, and even more after the variations that we have seen in SE GoM ( Godoy-Lozano et al, 2018 ), where we identified changes in the bacterial community possibly due to perturbations generated by anthropogenic oil activities. Sanchez-Soto et al (2018) , reported a similar bacterial community from the Perdido Fold Belt as in this work. In both reports we observe several coincidences at the Class, Order, and even at Genus level.…”

“…The Gulf of Mexico (GoM) is a basin with one of the most significant oil reservoirs in the world. There are few microbial diversity studies in Mexican waters of the GoM ( Lizarrága-Partida, 1986 ; Rosano-Hernández et al, 2012 ; Sanchez-Soto et al, 2018 ; Ramírez et al, 2020 ) in contrast to an extensive effort along the northeastern coast, particularly related to the Deep Water Horizon oil spill ( Kostka et al, 2011 ; Liu et al, 2012 ; Mason et al, 2014 ). Worldwide, oceans’ microbiology has been studied principally throughout the water-column and hot-spots (i.e., seeps, hydrothermal vents, oil discharge sites, etc.).…”

Figure 1: Collection site locations.

“…Quero et al (2015) reported differences in community composition and the formation of two clusters corresponding to two coastal sites with significant differences in the environmental variables and levels of hydrocarbon contamination. Differences in sediment microbial communities have been detected between contrasting sites, such as shallow and deep marine zones (Godoy-Lozano et al, 2018;Sánchez-Soto et al, 2018), water versus sediment samples (Reyes-Sosa, Apodaca-Hernández & Arena-Ortiz, 2018;Ul-Hasan et al, 2019), sediment from different marine ecosystems (lagoon, sea, wetlands, freshwater upwelling) (Reyes-Sosa, Apodaca-Hernández & Arena-Ortiz, 2018), and in microcosm experiments with hydrocarbons added in different concentrations (Bacosa et al, 2018;Wang et al, 2016). We found no clustering by site or season, with a high intra-variation between samples.…”

“…Bacterial diversity decreases with the increase in hydrocarbon content in sediment (Korlević et al, 2015;LaMontagne et al, 2004;Quero et al, 2015) and specific bacterial groups become dominant (Bacosa et al, 2018;Harayama, Kasai & Hara, 2004;Kessler et al, 2011;Mason et al, 2014b;Mason et al, 2014a;Mason et al, 2012;Valentine et al, 2010). There are numerous studies on the effect of hydrocarbon pollution in the microbial communities of sediments in the northern region the Gulf of Mexico (Bacosa, Liu & Erdner, 2015;Bacosa et al, 2018;Dong et al, 2019;Liu, Bacosa & Liu, 2017;Liu & Liu, 2013;Mason et al, 2014b;Mason et al, 2014a;Ramírez et al, 2020;Sánchez-Soto et al, 2018). However, information concerning the southern part of this area is lacking.…”