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POTENTIAL MICROBIAL DETOXIFIERS of Mehg in BARCELONA CITY CONTINENTAL SHELF

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POTENTIAL MICROBIAL DETOXIFIERS of Mehg in BARCELONA CITY CONTINENTAL SHELF POTENTIAL MICROBIAL DETOXIFIERS OF MeHg IN BARCELONA CITY CONTINENTAL SHELF TREBALL REALITZAT PER Marina Pérez García PER OBTENIR EL TÍTOL DE Màster en Microbiologia Avançada 2017-2018 Treball de Final de Màster realitzat sota la supervisió la Dra Silvia González-Acinas i la Dra Andrea García Bravo a l’Institut de Ciències del Mar (ICM-CSIC) Barcelona, 03 de Setembre de 2018 POTENTIAL MICROBIAL DETOXIFIERS OF MeHg IN BARCELONA CITY CONTINENTAL SHELF TREBALL REALITZAT PER Marina Pérez García PER OBTENIR EL TÍTOL DE Màster en Microbiologia Avançada 2017-2018 Treball de Final de Màster realitzat sota la supervisió la Dra Silvia González-Acinas i la Dra Andrea García Bravo a l’Institut de Ciències del Mar (ICM-CSIC) Barcelona, 03 de Setembre de 2018 Silvia González-Acinas Marina Pérez García Andrea García Bravo Abstract Mercury specially in the form of Methylmercury (MeHg) is a big concern because affects human and wildlife health and accumulates and biomagnified in the aquatics systems through the food chain. Some Bacteria and Archaea have evolved resistance mechanisms to mercury compounds, this resistance is encoded in the mer operon. So, the microorganisms that have merA and merB genes can completely transform the neurotoxic form of MeHg in the volatile form of mercury. Despite the persistence of mercury there is no information about the mercury detoxification processes in Barcelona continental shelf. Therefore, the aim of this study is to detect the presence of merA and merB in past (1987 and 2008) and present (from two months April and May 2018) sediment samples from the Barcelona continental shelf. For this task we performed DNA and RNA extractions and amplification of 16S PCR to detect the presence of microbial DNA. Since there is not currently specific primers for merA and merB genes targeting microbial taxa from contaminated sediment microorganisms, we have designed a pool of 10 specific primers for 5 microorganisms that could potentially be in the sediments and present these genes. Of those, we have detected the possible presence of merB genes related to Rhodococcus, Pseudomonas and Desulfovibrio in the sediments samples from fresh (2018) and 2008 samples. Future validation by sequencing those merB PCR amplicons would be done in a next step as well as the attempt to isolate those microorganisms in pure culture. Table of contents 1. Introduction…………………………………………………………………….1 2. Objectives of this study……………………………………………………….5 3. Materials and methods………………………………………………………..6 3.1 Sediment samples………………………………………………………...6 3.2 MeHg analyses…………………………………………………………….7 3.3 DNA and RNA extractions and quantifications………………………...7 3.4 Amplification of the 16S rRNA gene by PCR………………………….10 3.5 In silico analyses of the merAB genes from public available bacterial and archaeal genomes………………………………………..11 3.6 Primer design of merA and merB genes of sediment bacterial representative taxa……………………………………………12 3.7 Testing the amplification with the designed merAB primers in sediment samples…………………………………………….12 4. Results………………………………………………………………………….13 4.1 Extractions…………………………………………………………………13 4.2 Amplification of the 16S rRNA gene in sediment samples…………...13 4.3 Bacteria and archaea genomes with merA and merB genes……………………………………………………………………….15 4.4 Primers design…………………………………………………………….15 4.5 Amplification of merA and merB genes…………………………………20 5. Discussion and conclusions…………………………………………………..22 6. Bibliography…………………………………………………………………….24 1. Introduction Mercury is emitted from both natural and anthropogenic sources. The natural sources include volcanic activity, weathering of rock and, biomass burning, such as vegetation. Nowadays, most of mercury found in the atmosphere is emitted by anthropogenic activities and represents 2/3 of all sources of mercury. The major anthropogenic source is combustion of fossil fuels, especially coal. Other industrial processes that release mercury to the atmosphere are cement production, iron and steel production, chlor-alkali facilities, gold production, waste disposal, mercury mining and re-emission of previously deposited anthropogenic mercury (Kim & Zoh, 2012. Selin, 2009) (Amos et al., 2013). In the past few decades mercury emissions in the United States and Europe have declined but, emissions from Asia continue to increase, representing more than the 50% of global anthropogenic emissions. As a consequence of anthropogenic perturbations to the global mercury cycle, mercury content of surface ocean waters have tripled compared to pre-anthropogenic conditions (Lamborg et al., 2014). Mercury can be found in the environment as inorganic and organic mercury species. Inorganic mercury can exist in two oxidation states; Hg(0) (metallic, zero oxidation state, elemental form) and Hg(II) (mercuric, oxidation state +2, divalent mercury) in the environment. Another species in the atmosphere is particulate mercury Hg(p), which is the mercury species adsorbed by particulate matter (Kim & Zoh, 2012). Mercury has a complex biogeochemical cycle (Figure 1). Hg(0) is the most abundant form of mercury in the atmosphere, has a low solubility in water and its main sink is oxidation to Hg (II). Hg (II) and Hg(P) are more soluble in water and are the predominant forms of mercury deposited to ecosystems through wet and dry deposition. (Selin, 2009). In general, Hg (II) is delivered to the ocean via either rivers and/or direct atmospheric deposition and is either reduced to Hg(0), with potential evasion to the atmosphere, scavenged by organic-rich particles resulting in deposition to sediments or converted to the more toxic form of methylmercury (MeHg). (Fitzgerald, Lamborg, & Hammerschmidt, 2007) 1 Figure 1: Biogeochemical cycle of mercury in a multimedia environment. (Kim & Zoh, 2012) This methylation of inorganic mercury Hg(II) to the organic form methylmercury (is a biologically mediated process known to be facilitated by some strains of sulfate- and iron reducing bacteria, acetogenic bacteria and methanogens (Gilmour et al., 2013; Parks et al., 2013). It primarily occurs under oxygen limited conditions such as those of water columns (Eckley et al., 2005; Malcolm et al., 2010), sediments (Bouchet et al., 2013; Bravo et al., 2015; Drott et al., 2008; Hines et al., 2012; Jonsson et al., 2014; Liem- Nguyen et al., 2016) and flooded soils such as wetlands (Louis et al., 1996; Tjerngren et al., 2012; Windham-Myers et al., 2014), ponds (Herrero Ortega et al., 2018; Lehnherr et al., 2012; MacMillan et al., 2015) (Herrero Ortega et al., 2018) but also in microenvironments such as periphyton, macrophytes (Achá et al., 2011; Cleckner et al., 1999; Guimarães et al., 2006; Hamelin et al., 2011; Mauro et al., 2002) or settling particles of oxic water columns (Cossa et al., 2009; Gascón Díez et al., 2016; Lehnherr et al., 2011; Monperrus et al., 2007; Sunderland et al., 2009). Methylmercury is a big concern because is a potent neurotoxin that affects human and wildlife development and health. Methylmercury accumulates in the aquatic food webs because can bioconcentrate in living organisms and then further biomagnified up the food chain (Mason et al., 2012). The effects of MeHg are especially dangerous for pregnant women because the transfer of MeHg from a maternal seafood diet to prenatal life stages can inhibit the neurological and cardiovascular development of children. Additionally, MeHg may affect adversely the cardiovascular health of adults who eat fish. (Clarkson and Magos, 2006) 2 Some Bacteria and Archaea have evolved resistance mechanisms to mercury compounds. The Hg resistance (mer) system is encoded by the mer operon which is one of the most widely distributed Hg(II) and Methylmercury detoxification genetic system. The mer operon can encode for two enzimes: merA and/or merB. MerA (homodimeric flavindependent disulfide oxidoreductase enzyme mercuric reductase) catalyzes the reduction of the highly toxic ionic Hg(II) into less toxic and volatile Hg(0) in a NAD(P)H- dependent reaction (Barkay et al., 2003). This reduction is one of the most influential biogeochemical transformations in the mercury cycle because result in evasion of the volatile elemental form from the ocean (Fitzgerald, Lamborg, & Hammerschmidt, 2007). The mer operon may also encode for merB (organomercury lyase) which demethylates MeHg into Hg(II). Aside from merA and merB the mer operon may also encode for genes with the function of transport and regulation of the operon like a periplasmic Hg(II) scavenging protein (MerP), one or more inner membrane spanning proteins (MerT, MerC, MerE, MerF, MerG) that transport Hg(II) to the cytoplasm where it is reduced by MerA, and one or two regulatory proteins (MerR, MerD). The overall expression of mer is regulated by MerR, acting as a transcriptional repressor or activator in the absence and presence of Hg(II), respectively. In addition, several proteobacteria encode for MerD which functions to downregulate operon expression (Barkay et al.,2003; Lin et al.,2012) (Figure 2). Therefore, there are mainly two types of mercury operon, the “narrow spectrum” which only merA gene is present and resistance mechanism is limited to enzymatic detoxification of only inorganic mercury compound and” broad spectrum” which contain the extra gene merB and exhibited resistance to inorganic and organic mercurial compounds forms by converting both to their volatile form (Sadhukhan et al. 1997). So the microorganisms that have merA and merB genes can completely transform the toxic form of MeHg in the volatile form Hg0. MerB acts first and
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