Community Structure and Abundance of Archaea in a Zostera marina Meadow: A Comparison between Seagrass-Colonized and Bare Sediment Sites

Abstract

Seagrass colonization alters sediment physicochemical properties by depositing seagrass fibers and releasing organic carbon and oxygen from the roots. How this seagrass colonization-induced spatial heterogeneity affects archaeal community structure and abundance remains unclear. In this study, we investigated archaeal abundance, diversity, and composition in both vegetated and adjacent bare surface sediments of a Zostera marina meadow. High-throughput sequencing of 16S rDNA showed that Woesearchaeota, Bathyarchaeota, and Thaumarchaeota were the most abundant phyla across all samples, accounting for approximately 42%, 21%, and 17% of the total archaeal communities, respectively. In terms of relative abundance, Woesearchaeota and Bathyarchaeota were not significantly different between these two niches; however, specific subclades (Woese-3, Woese-21, Bathy-6, Bathy-18) were significantly enriched in vegetated sediments (P < 0.05), while Thaumarchaeota was favored in unvegetated sites (P = 0.02). The quantification of archaeal 16S rRNA genes showed that the absolute abundance of the whole archaeal community, Bathyarchaeota, and Woese-3, Woese-10, Woese-13, and Woese-21 was significantly more abundant in vegetated sediments than in bare sediments (P < 0.05). Our study expands the available knowledge of the distribution patterns and niche preferences of archaea in seagrass systems, especially for the different subclades of Woesearchaeota and Bathyarchaeota, in terms of both relative proportions and absolute quantities.

Effects of Organic Phosphorus on Methylotrophic Methanogenesis in Coastal Lagoon Sediments With Seagrass (Zostera marina) Colonization

“…These findings are consistent with our knowledge that the surface layer sediments colonized by the seagrass Z. marina provide more bioavailable organic matter (Sun et al, 2015;Zheng et al, 2019), such as methylated compound, that serve as a substrate for methanogens. Methylotrophic methanogens were able to outcompete SRB by virtue of excess substrate by which they maintained higher activity in the surface layer sediments; thus, it was reasonable that phytate phosphorus would not affect methane production to a great extent.…”

“…Among different substrates utilized by methanogens, marine methylated compounds, such as methanol and mono-, di-, or trimethylamines, are major substrates for methane production by methylotrophic methanogens. The primary sources of methylated compound substrates are the microbial decomposition of marine organisms or the root exudates of plants such as mangroves, Spartina alterniflora Loisel, and seagrasses ( Mohanraju and Natarajan, 1992 ; Lyimo et al, 2009 ; Sun et al, 2015 ; Yang et al, 2019 ; Zheng et al, 2019 ). These substrates are not routinely used by SRB in the presence of methanogens ( Lyimo et al, 2009 ), but promote the rapid growth of methylotrophic methanogens in sediments with high densities of seaweed.…”

“…Although organic and inorganic contaminants in SL have been comprehensively investigated, the microorganisms and possible biochemical reactions involved are poorly understood. Furthermore, recent studies have provided evidence that populations of diazotrophic sulfate-reducing bacteria and archaea such as specific subclades of Woesearchaeota and Bathyarchaeota , as well as methanogens, more frequently occur in surface sediments colonized by Z. marina seagrass meadows than in bare sediments ( Sun et al, 2015 ; Zheng et al, 2019 ). This may be related to the fact that Z. marina seagrass meadows can provide more bioavailable organic matter.…”

The Seagrass Holobiont: What We Know and What We Still Need to Disclose for Its Possible Use as an Ecological Indicator

“…A similar paucity of information turns evident also considering the association of seagrass with viruses and archaea, even if, for the latter, the existence of both Euryarchaeota and Crenarchaeota in sediments associated with different Zostera spp. has been reported [203,206].…”

“…can be quite easily replicated in vitro, biotic factors are much more difficult to mimic. In addition, evidence from culture dependent and microscopic approaches underscore a prominent role of fungi within seagrass physiology and ecology [203][204][205], but studies providing a wide overview of these taxa, such as those employing NGS approaches, are still incipient [27,80,206,207]. A similar paucity of information turns evident also considering the association of seagrass with viruses and archaea, even if, for the latter, the existence of both Euryarchaeota and Crenarchaeota in sediments associated with different Zostera spp.…”