Diversity of Archaea in Marine Sediments from Skan Bay, Alaska, Including Cultivated Methanogens, and Description of Methanogenium boonei sp. nov

Abstract

Methanogenesis in cold marine sediments is a globally important process leading to methane hydrate deposits, cold seeps, physical instability of sediment, and atmospheric methane emissions. We employed a multidisciplinary approach that combined culture-dependent and -independent analyses with geochemical measurements in the sediments of Skan Bay, Alaska (53°N, 167°W), to investigate methanogenesis there. Cultivation-independent analyses of the archaeal community revealed that uncultivated microbes of the kingdoms Euryarchaeota and Crenarchaeota are present at Skan Bay and that methanogens constituted a small proportion of the archaeal community. Methanogens were cultivated from depths of 0 to 60 cm in the sediments, and several strains related to the orders Methanomicrobiales and Methanosarcinales were isolated. Isolates were psychrotolerant marine-adapted strains and included an aceticlastic methanogen, strain AK-6, as well as three strains of CO 2 -reducing methanogens: AK-3, AK7, and AK-8. The phylogenetic positions and physiological characteristics of these strains are described. We propose a new species, Methanogenium boonei, with strain AK-7 as the type strain.More than 85% of the ocean's organic carbon is deposited in shallow, anoxic marine sediments (8). Methanogens play an important role in the degradation of this organic matter by converting low-molecular-weight compounds into methane. In marine sediments, methane is present in dissolved form in the pore water, as free gas, or trapped within methane hydrates. Molecular and isotopic data suggest that most of the methane produced in marine sediments is of biogenic origin (31); however, methanogens that inhabit permanently cold marine sediments have been poorly characterized.Several studies have investigated the microbial diversity in cold marine sediments (12,43,46); however, the role that these microbes play in mediating geochemical processes is still not completely understood. In addition to methanogens, uncultivated lineages of other Archaea have been identified in marine sediments (22,29,32,37,41,67). These include phylotypes belonging to the marine benthic groups B (MBG-B), C, and D and the anaerobic methane-oxidizing (ANME) archaeal groups ANME-1 and ANME-2.Skan Bay has previously served as a model system for studying low-temperature microbial processes in marine sediments (2,3,47,51,66). The sediments contain clear environmental gradients (66), and the complete redox sequence from oxygen to methane occurs within 0.5 m of the surface, allowing for good depth resolution of microbial activities (20). Previous analyses of Skan Bay sediments have shown that microbes mediate important geochemical processes, including sulfate reduction, methane production, and the anaerobic oxidation of methane (AOM) (66). The specific aim of this study was to identify and cultivate Archaea involved in methane cycling at Skan Bay. Cultivation-independent and -dependent techniques were employed to characterize the archaeal populations at various depths and therefore along...

Temporal evolution of methane cycling and phylogenetic diversity of archaea in sediments from a deep-sea whale-fall in Monterey Canyon, California

“…In these studies, up to 60% of clones in typical deep-sea sediments were Crenarchaeota MGI and, similarly, phylotypes representing the Crenarchaeota MBGB have been recovered from subsurface marine sediments (Vetriani et al, 1999;Dhillon et al, 2005;Knittel et al, 2005;Kendall et al, 2007). Similar diversity was recovered in our study, with Figure 8 Phylogenetic relationships of archaea associated with a 2893 m whale-fall in Monterey Canyon (CA), based on amino-acid divergence (166 amino acids) within a region of the methyl-coenzyme M reductase (mcrA) gene, to selected cultured and environmental sequences in public databases.…”

“…The dominant Crenarchaeota MBGB phylotype (R33_10d_E11), present only in the deeper 12-15 cm layer of the reference core, was 98% similar to an uncultured archaeon from deepsea sediments in the Atlantic Ocean (Table 3 and Figure 5; Vetriani et al, 1999). Phylotypes related to the Euryarchaeota were also found only in the 12-15 cm layer (representing up to 24% of the recovered phylotypes; Table 3 including a phylotype (R33_10d_G1) related to uncultured Euryarchaeota from sediments in Skan Bay, Alaska and other members of the Thermoplasmatales-related marine benthic group D, (Girguis et al, 2003;Kendall et al, 2007). Additional, as yet unclassified Crenarchaeota (for example, R33_0s_F10), related to freshwater and soil archaea (Bintrim et al, 1997;Stein et al, 2002), made up the remainder of the sequence diversity (11% ; Table 3 and Figure 4).…”

Prokaryotic diversity, distribution, and insights into their role in biogeochemical cycling in marine basalts

“…However, Lysnes et al (2004) reported that methane was evolved in enrichment cultures inoculated with marine basalts. Although the Marine Benthic Group B clade currently lacks a cultured representative (Knittel et al, 2005), they are frequently associated with environments dominated by methane, methanogens and methanotrophs (Knittel et al, 2005;Kendall and Boone, 2006;Kendall et al, 2007). The role of this clade in the environment is unknown, but it is plausible that they are involved in methane biogeochemical cycling.…”

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).…”