Diversity and identification of methanogenic archaea and sulphate-reducing bacteria in sediments from a pristine tropical mangrove

Abstract

Mangrove sediments are anaerobic ecosystems rich in organic matter. This environment is optimal for anaerobic microorganisms, such as sulphate-reducing bacteria and methanogenic archaea, which are responsible for nutrient cycling. In this study, the diversity of these two functional guilds was evaluated in a pristine mangrove forest using denaturing gradient gel electrophoresis (DGGE) and clone library sequencing in a 50 cm vertical profile sampled every 5.0 cm. DGGE profiles indicated that both groups presented higher richness in shallow samples (0-30 cm) with a steep decrease in richness beyond that depth. According to redundancy analysis, this alteration significantly correlated with a decrease in the amount of organic matter. Clone library sequencing indicated that depth had a strong effect on the selection of dissimilatory sulphate reductase (dsrB) operational taxonomic units (OTUs), as indicated by the small number of shared OTUs found in shallow (0.0 cm) and deep (40.0 cm) libraries. On the other hand, methyl coenzyme-M reductase (mcrA) libraries indicated that most of the OTUs found in the shallow library were present in the deep library. These results show that these two guilds co-exist in these mangrove sediments and indicate important roles for these organisms in nutrient cycling within this ecosystem.

Archaeal communities in the sediments of different mangrove stands at Dongzhaigang, China

“…5 Pearson correlation coefficient of dominant genera with environmental variables shown in a heatmap dominant (Zhichao et al 2015). Most mcrA OTUs found in a pristine tropical mangrove were similar to the mcrA of Methanopyrus kandlery, and Methanothermococcus thermolithotrophicus, while only one OTU clustered close to the Methanosarcina cluster (Taketani et al 2010). Taken together, these results indicated that mangrove sediment ecosystems supported a diverse methanogen community even though their community differed in different sediment conditions.…”

“…Mangroves provide a unique ecological environment for diverse microbial communities (Kathiresan and Bingham 2001), including Archaea, the third domain of life that are often found in a wide range of environments (Chaban et al 2006). To date, studies focused on Archaea in mangrove ecosystems have dealt mainly with archaeal communities (Yan et al 2006;Rooney-Varga et al 2007;Pires 2010;Mendes et al 2012;Pires et al 2012;Tian et al 2012;Bhattacharyya et al 2015), methanogenic archaea (Mohanraju and Natarajan 1992;Lyimo et al 2000;Lyimo et al 2009;Taketani et al 2010), and ammoniaoxidizing archaea (Li et al 2011;Li and Gu 2013;Wang et al 2013;Wang and Gu 2014), but it still remains unclear whether there are differences in the composition, structure, and diversity of the archaeal communities in the sediments of different mangrove species.…”

Methane and sulfate dynamics in sediments from mangrove-dominated tropical coastal lagoons, Yucatán, Mexico

“…Secondly, methane may be produced in situ at these depths supported by a high abundance of competitive substrates in the sulfate reduction zone hence sustaining both methanogenesis and sulfate reduction (Holmer and Kristensen, 1994). Thirdly, methanogens may instead be able to thrive on various non-competitive substrates (Oremland and Polcin, 1982;Wellsbury and Parkes, 2000;Lee et al, 2008;Taketani et al, 2010). Indeed, use of non-competitive substrates by methanogens, including methanol, trimethylamines and dimethylsulfide, has been reported for mangrove sediments, coastal lagoons and continental shelf sediments (Ferdelman et al, 1997;Lyimo et al, 2000;Mohanraju et al, 1997;Purvaja and Ramesh, 2001;Torres-Alvarado et al, 2013;Maltby et al, 2016).…”

Descrição da comunidade microbiana ativa em solos de manguezais por metagenômica e metatranscriptômica

“…Essa diversidade pode variar com o local, a profundidade, a sazonalidade e as condições físicas e químicas do ambiente que exercem pressão seletiva sobre as comunidades, sua estrutura e funcionalidade MENDES et al, 2011;VARON-LOPEZ et al, 2014 (MENDES et al, 2012). As arquéias participam de forma significativa nos ciclos biogeoquímicos em manguezais, principalmente pela ação de grupos metanogênicos e oxidantes de amônio (VETRIANE et al, 1999, TAKETANI et al, 2010DIAS et al, 2011, MENDES et al, 2012 (MIRZA et al, 2014;VOSSENBERG et al, 2013) A fixação do nitrogênio é um dos processos biológicos mais importantes e essenciais para vida, atuando como principal processo de disponibilização de nitrogênio nos sistemas naturais (DIXON et al, 2004;SANTOS et al, 2012;VITOUSEK et al, 2012). Mais de 100 gêneros de bactérias e arquéias, que apresentam o gene nif, que codifica enzimas essenciais para o funcionamento do complexo nitrogenase (RAIMOND et al, 2004).…”

“…A melhor compreensão da função de arquéias nos ciclos biogeoquímicos contribui de forma significativa para entender o papel desses microrganismos para o fluxo energético nos manguezais, em processos como metanogênese, redução de sulfato, participando da oxidação da amônia, passo inicial para a nitrificação, além de ter muitas espécies que apresentam os genes ligados a fixação biológica de nitrogênio (OFFRE et al, 2014;TAKETANI et al, 2010;DIAS et al, 2011;VARON-LOPES et al, 2014 Uma das maiores limitações para o estudo ecológico das comunidades metabolicamente ativas esta no fato de o RNAm ser pouco representado numa amostra de RNA total extraído do solo, além do fato de que a vida do RNAm é curta em organismos procarióticos (CARVALHAES et al, 2012). Além disso, outras dificuldades são o acesso e lise das células microbianas, devido muitas células serem localizadas em micro-nichos entre as partículas do solo, absorção de RNAs por partículas do solo, além da atuação deletéria de RNAses, podem limitar est e tipo de estudo (CARVALHAES et al, 2012).…”