GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes

He, Zhili; Gentry, Terry J.; Schadt, Christopher W.; Wu, Liyou; Liebich, Jost; Chong, Song; Huang, Zhijian; Wu, Wei‐Min; Gu, Baohua; Jardine, P. M.; Criddle, Craig S.; Zhou, Jizhong

doi:10.1038/ismej.2007.2

Cited by 527 publications

(474 citation statements)

References 42 publications

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“…Triplicate of 500 g soil were placed in plastic pots and flooded with deionized water to maintain a 2 cm layer of standing water above the soil surface. A Rhizon soil solution sampler was inserted to each pot for the collection of soil pore water at 5,10,15,20,30, and 54 days after flooding. Soil pore water was acidified to pH <2 with HCl (10 mL solution with 0.1 mL concentrated HCl) and filtered through a sterilized 0.2 μm filter before analysis of As speciation.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

“…Soil redox potential (Eh) was measured at approximately 0.5 cm below the soil surface using a combined platinum and silver/silver chloride electrode system. Dissolved organic C (DOC) was measured in the pore water samples collected on day 30.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

“…The quantified microarray data were preprocessed as described previously. 30 ■ RESULTS Soil Properties. The six soils used in the present study varied widely in total As concentrations, ranging from 3 to 81 Table S1).…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

“…24,27 The amino acid sequences of arsM from divergent organisms are highly conserved, with three strictly conserved cysteine residues being involved in the catalytic function. 26,28 Lomax et al 29 used a microarray-based technique (GeoChip 4.0) 30 to detect microbial functional genes involved in As transformation in a contaminated paddy soil from Bangladesh. Thirty-five of the 66 arsM sequences included in the array were detected.…”

Section: ■ Introductionmentioning

confidence: 99%

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Arsenic Methylation in Soils and Its Relationship with Microbial arsM Abundance and Diversity, and As Speciation in Rice

Zhao

Harris

Jia

et al. 2013

Environ. Sci. Technol.

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Methylation of arsenic in soil influences its environmental behavior and accumulation by plants, but little is known about the factors affecting As methylation. As speciation was determined in the pore waters of six soils from diverse geographical locations over 54 days of incubation under flooded conditions. The concentration of methylated As (monomethylarsonic acid, MMA, and dimethylarsinic acid, DMA) varied from 0 to 85 μg L −1 (0 − 69% of the total As in pore water). Two Bangladeshi paddy soils contaminated by irrigation of As-laden groundwater produced large concentrations of inorganic As but relatively little methylated As. Two contaminated paddy soils from China produced a transient peak of DMA during the early phase of incubation. Methylated As represented considerable proportions of the total soluble As in the two uncontaminated soils from the UK and U.S. The copy number of the microbial arsenite methyltransferase gene (arsM) correlated positively with soil pH. However, pore-water methylated As correlated negatively with pH or arsM copy number, and positively with dissolved organic C. GeoChip assay revealed considerable arsM diversity among the six soils, with 27−35 out of 66 sequences in the microarray being detected. As speciation in rice plants grown in the soils generally mirrored that in the pore water. The results suggest that methylated As species in plants originated from the soil and As methylation in soil was influenced strongly by the soil conditions. ■ INTRODUCTIONArsenic (As) is a ubiquitous contaminant in the environment originating from both natural and anthropogenic sources. Because its biogeochemical behavior and toxicity vary greatly among different chemical species, it is important to understand how the speciation of As changes in the environment and what drives such changes. A particularly important case is the paddy rice system because it is now recognized that rice is a major source of As in the human diet. 1 The anaerobic conditions in paddy soils are conducive to the mobilization of arsenite, 2,3 which is taken up inadvertently by rice roots through the strong uptake pathway for silicic acid. 4 Rice grain contains both inorganic As (arsenate and arsenite) and organic As (mostly dimethylarsinic acid, DMA; occasionally also trace amounts of monomethylarsonic acid, MMA, and tetramethylarsonium). 5−9 As speciation in rice varies widely among different riceproducing regions. Market-basket surveys show that Asian rice generally is dominated by inorganic As with DMA typically accounting for about 20% of the total As. [5][6][7]10 In contrast, rice produced in the U.S. and Europe is more variable in As speciation with many samples containing more organic than inorganic As. 5,7,8,10 It is possible that that this geographical pattern reflects the relative bioavailability of inorganic versus organic As in different paddy environments. 10 Compared with inorganic As, methylated As species are more easily accumulated in rice grain. 10 Although pentavalent methylated As species are ...

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Section: ■ Materials and Methodsmentioning

confidence: 99%

Section: ■ Materials and Methodsmentioning

confidence: 99%

Section: ■ Materials and Methodsmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Arsenic Methylation in Soils and Its Relationship with Microbial arsM Abundance and Diversity, and As Speciation in Rice

Zhao

Harris

Jia

et al. 2013

Environ. Sci. Technol.

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187

125

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“…It's been demonstrated that microarray has a power equal to new generation sequencing (Claesson et al, 2009). Several types of microarrays have been used to identify the gut microorganisms, like community genome array, functional genome array and phylogenetic oligonucleotide array (Loy et Wu et al, 2004;He et al, 2007). Recently, Paliy et al developed a more sensitive microarray containing Affymetrix GeneChip platform containing 775 representative sequences of phylospecies clusters obtained from human feces and several colon sites and was able to detect bacterial DNA present at the level of 0.00025% of the total community DNA (Paliy et al, 2009).…”

Section: Microarraymentioning

confidence: 99%

The role of gut microbiota in the gut-brain axis: current challenges and perspectives

2013

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Brain and the gastrointestinal (GI) tract are intimately connected to form a bidirectional neurohumoral communication system. The communication between gut and brain, knows as the gut-brain axis, is so well established that the functional status of gut is always related to the condition of brain. The researches on the gut-brain axis were traditionally focused on the psychological status affecting the function of the GI tract. However, recent evidences showed that gut microbiota communicates with the brain via the gut-brain axis to modulate brain development and behavioral phenotypes. These recent fi ndings on the new role of gut microbiota in the gut-brain axis implicate that gut microbiota could associate with brain functions as well as neurological diseases via the gut-brain axis. To elucidate the role of gut microbiota in the gut-brain axis, precise identification of the composition of microbes constituting gut microbiota is an essential step. However, identifi cation of microbes constituting gut microbiota has been the main technological challenge currently due to massive amount of intestinal microbes and the diffi culties in culture of gut microbes. Current methods for identifi cation of microbes constituting gut microbiota are dependent on omics analysis methods by using advanced high tech equipment. Here, we review the association of gut microbiota with the gut-brain axis, including the pros and cons of the current high throughput methods for identifi cation of microbes constituting gut microbiota to elucidate the role of gut microbiota in the gut-brain axis.

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Chlorinated Hydrocarbon Metabolism

Reineke¹,

Mandt²,

Kaschabek³

et al. 2011

Encyclopedia of Life Sciences

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The widespread global distribution of chlorinated hydrocarbons, their high lipophilicity and their recalcitrance have contributed to their importance as environmental toxicants. Their metabolism under oxic and anoxic conditions mediated by prokaryotic and eukaryotic cells is discussed. Various aerobic bacteria are able to use chlorinated hydrocarbons as the sole source of carbon and energy and some anaerobic bacteria can use some of these as an artificial electron acceptor in reductive dechlorination. Liver enzymes are responsible for the formation of hydrophilic metabolites ready for excretion which often lead to highly reactive and potentially toxic intermediates. Whereas fungi, especially ligninolytic ones, usually only exhibit ‘side activities’ for chlorinated hydrocarbons. The capabilities of bacteria had led to the development of various bioremediation processes. Both, successes and failures within these processes are known. Therefore, current research aims at a better understanding of global community interactions. Key Concepts: Chlorinated hydrocarbons have been produced by the chemical industry since nearly a decade in large amounts, but they can also be observed as natural compounds, sometimes exceeding the industrially produced amounts. Even though toxicological properties have pushed the chlorochemistry into the focus of considerable debate and governmental regulatory action, chlorinated hydrocarbons remain essential for certain applications. The aerobic metabolism of chlorinated hydrocarbons by bacteria has been studied in detail and an immense amount of information is available on pathways, enzymes and genes involved in the mineralisation of chloroaromatics. The anaerobic degradation of chlorinated hydrocarbons is due to the capablity of anaerobic bacteria to use them in anaerobic respiration, which results in dechlorination. Dehalococcoides organisms are the most versatile reductive dehalogenators as being capable to dehalogenate chlorinated dioxins, biphenyls, benzenes and vinyl chloride, among others. Microbial activities have been widespread used for bioremediation purposes through natural attenuation, biostimulation and bioaugmentation. The poor understanding of the functioning of the complex microbial activities in situ made bioremediation efforts quite unreliable. The rapid development of molecular techniques in recent years allows immense insights into the processes in situ , but also on the overall physiology of biocatalysts.

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GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes

Cited by 527 publications

References 42 publications

Arsenic Methylation in Soils and Its Relationship with Microbial arsM Abundance and Diversity, and As Speciation in Rice

Arsenic Methylation in Soils and Its Relationship with Microbial arsM Abundance and Diversity, and As Speciation in Rice

The role of gut microbiota in the gut-brain axis: current challenges and perspectives

Chlorinated Hydrocarbon Metabolism

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