Specific Bacterial, Archaeal, and Eukaryotic Communities in Tidal-Flat Sediments along a Vertical Profile of Several Meters

Abstract

The subsurface of a tidal-flat sediment was analyzed down to 360 cm in depth by molecular and geochemical methods. A community structure analysis of all three domains of life was performed using domain-specific PCR followed by denaturing gradient gel electrophoresis analysis and sequencing of characteristic bands. The sediment column comprised horizons easily distinguishable by lithology that were deposited in intertidal and salt marsh environments. The pore water profile was characterized by a subsurface sulfate peak at a depth of about 250 cm. Methane and sulfate profiles were opposed, showing increased methane concentrations in the sulfate-free layers. The availability of organic carbon appeared to have the most pronounced effect on the bacterial community composition in deeper sediment layers. In general, the bacterial community was dominated by fermenters and syntrophic bacteria. The depth distribution of methanogenic archaea correlated with the sulfate profile and could be explained by electron donor competition with sulfate-reducing bacteria. Sequences affiliated with the typically hydrogenotrophic Methanomicrobiales were present in sulfate-free layers. Archaea belonging to the Methanosarcinales that utilize noncompetitive substrates were found along the entire anoxic-sediment column. Primers targeting the eukaryotic 18S rRNA gene revealed the presence of a subset of archaeal sequences in the deeper part of the sediment cores. The phylogenetic distance to other archaeal sequences indicates that these organisms represent a new phylogenetic group, proposed as "tidal-flat cluster 1." Eukarya were still detectable at 360 cm, even though their diversity decreased with depth. Most of the eukaryotic sequences were distantly related to those of grazers and deposit feeders.It has been estimated, that marine subsurface habitats harbor the majority of the global prokaryotic biomass (55). Despite the inhospitality of subsurface sites, remarkably diverse microbial communities were found within the deep biosphere tens to hundreds of meters below the seafloor (15, 31). Microbiological investigations on marine subsurface communities mainly focused on the deep biosphere in open-ocean and continental-margin sediments (8, 34). So far, little attention has been paid to the subsurface of coastal sediments (49), but the number of publications is increasing (23,29,56).Tidal flats are characterized by high primary production rates and consequently intense remineralization in the sediment (10, 38, 39). Furthermore, they exhibit high sedimentation rates and, in contrast to open-ocean sites (8, 35), steep chemical gradients, with oxygen generally being depleted within a few millimeters below the sediment surface (2). Nevertheless, tidal-flat sediments show a strong patchiness as oxic microniches can be found down to a depth of 20 cm along the burrows of the zoobenthos (40). In layers beneath, however, microbial processes are strictly anaerobic and seem to be governed by the sequence of electron acceptors along the redox series, wit...

Degradation of cyanobacterial biomass in anoxic tidal-flat sediments: a microcosm study of metabolic processes and community changes

“…In the control experiment without Spirulina addition, the same amount of sulfide was built as in the stimulated experiment. Although the sulfate-reducing organisms and the archaeal community were already investigated in previous studies (Wilms et al, 2006b(Wilms et al, , 2007, our study focused on the initial steps of degradation.…”

“…As sulfate reducers and methanogens can be easily detected by specific important genes, which either encode for the dissimilatory sulfate reductase or the methyl-coenzyme M reductase, the recent studies focused on these groups (Wilms et al, 2007). It is well known that the terminal oxidizers make only a minor part of the community, whereas the fermentative microorganisms are more abundant (Schink, 2002;Kö pke et al, 2005;Wilms et al, 2006b). Thus, owing to a lack of a fermentation important gene, the largest part of the community remains unexplored.…”

Origin of a major infectious disease in vertebrates: The timing ofCryptosporidiumevolution and its hosts

“…tidal-flat (Wilms et al 2006) and ballast water (Pagenkopp et al 2016). Cryptosporidium 'struthionis' is on a relatively long branch with seemingly phylogenetically deep origins.…”

Community Structure, Diversity, and Vertical Distribution of Archaea Revealed by 16S rRNA Gene Analysis in the Deep Sea Sediment of the Ulleung Basin, East Sea

“…E-mail : hyunjh@hanyang.ac.kr 행되어왔다 (Gray and Herwig 1996;Ravenschlag et al 1999). 그러나 최근 분자생태기술의 발달을 통하여 제한된 환경에서만 서식한다고 알려져 있던 고세균이 일반 해양 환경 및 심해 퇴적물 (Vetriani et al 1999;Reed et al 2002;Inagaki et al 2003;Newberry et al 2004;Biddle et al 2006;Inagaki et al 2006), 남극 퇴적물 (Bowman and McCuaig 2003;Kendall et al 2007), 냉용수(cold seep)지역 (Knittel et al 2005;Arakawa et al 2006), 메탄 누출(methane seep)지역 (Lloyd et al 2006;Dang et al 2009), 해저 열수구(hydrothermal vent)지역 (Takai and Horikoshi 1999;Reysenbach et al 2000;Teske et al 2002), 빈영양(organic-poor)해역 (Sørensen et al 2004), 갯 벌(tidal flat) (Wilms et al 2006) 및 염습지(salt marsh) (Nelson et al 2009)와 같은 다양한 해양환경에서 광범위 하게 분포하고 있음이 밝혀졌으며, 이를 바탕으로, 고세균 도 진정세균과 마찬가지로 해양 퇴적물에서 생지화학적 물질순환에 중요한 역할을 담당하는 것으로 인식되고 있 다 (Knittel et al 2005;Biddle et al 2006;Hallam et al 2006;Nicol and Schleper 2006).…”