Lucia Cavalca

University of Milan

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V. Andreoni

University of Milan

A. Corsini

University of Milan

Sarah Zecchin

University of Milan

P. Zaccheo

University of Milan

Gerard Muyzer

University of Amsterdam

Milena Colombo

University of Milan

M. Colombo

MRC Weatherall Institute of Molecular Medicine

E. Dell’Amico

University of Milan

R. Zanchi

University of Milan

Henrique Ferreira

Universidade Estadual Paulista (Unesp)

Cooperative Institutions

University of Milan

Universidade Estadual Paulista (Unesp)

Universidade de São Paulo

University of Naples Federico II

Istituto di Biologia e Biotecnologia Agraria

National Research Council

Universidade de Vigo

Universidad de La Frontera

University of Groningen

Centre de Microbiologie du Sol et de l'Environnement

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Arsenic-resistant bacteria associated with roots of the wild Cirsium arvense (L.) plant from an arsenic polluted soil, and screening of potential plant growth-promoting characteristics

Systematic and Applied Microbiology (2010)

Lucia Cavalca R. Zanchi A. Corsini Milena Colombo Cristina Romagnoli

Alphaproteobacteria

Betaproteobacteria

Microbacterium

10.1016/j.syapm.2010.02.004

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Citations (132)

Effect of carbon content and sulfate fertilization on thioarsenate biogeochemistry and on rhizosphere microbiome in rice paddies

Sarah Zecchin W. Jiajia María Martínez‐Mena Rudinei De Marco P. Britta

Biogeochemistry

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Rhizosphere colonization and arsenic translocation in sunflower (Helianthus annuus L.) by arsenate reducing Alcaligenes sp. strain Dhal-L

World Journal of Microbiology and Biotechnology (2013)

Lucia Cavalca A. Corsini Sachin P. Bachate V. Andreoni

Alcaligenes

Strain (injury)

Helianthus annuus

10.1007/s11274-013-1359-4

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Citations (16)

Phylogenetic Structure and Metabolic Properties of Microbial Communities in Arsenic-Rich Waters of Geothermal Origin

Frontiers in Microbiology (2017)

Simona Crognale Sarah Zecchin Stefano Amalfitano Stefano Fazi Barbara Casentini

Arsenic (As) is a toxic element released in aquatic environments by geogenic processes or anthropic activities. To counteract its toxicity, several microorganisms have developed mechanisms to tolerate and utilize it for respiratory metabolism. However, still little is known about identity and physiological properties of microorganisms exposed to natural high levels of As and the role they play in As transformation and mobilization processes. This work aims to explore the phylogenetic composition and functional properties of aquatic microbial communities in As-rich freshwater environments of geothermal origin and to elucidate the key microbial functional groups that directly or indirectly may influence As-transformations across a natural range of geogenic arsenic contamination. Distinct bacterial communities in terms of composition and metabolisms were found. Members of Proteobacteria, affiliated to Alpha- and Betaproteobacteria were mainly retrieved in groundwaters and surface waters, whereas Gammaproteobacteria were the main component in thermal waters. Most of the OTUs from thermal waters were only distantly related to 16S rRNA gene sequences of known taxa, indicating the occurrence of bacterial biodiversity so far unexplored. Nitrate and sulphate reduction and heterotrophic As(III)-oxidization were found as main metabolic traits of the microbial cultivable fraction in such environments. No growth of autotrophic As(III)-oxidizers, autotrophic and heterotrophic As(V)-reducers, Fe-reducers and oxidizers, Mn-reducers and sulfide oxidizers was observed. The ars genes, involved in As(V) detoxifying reduction, were found in all samples whereas aioA (As(III) oxidase) and arrA genes (As(V) respiratory reductase) were not found. Overall, we found that As detoxification processes prevailed over As metabolic processes, concomitantly with the intriguing occurrence of novel thermophiles able to tolerate high levels of As.

Betaproteobacteria

Autotroph

Extreme environment

Alphaproteobacteria

10.3389/fmicb.2017.02468

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Citations (21)

Assessing arsenic bioremediation potential of epilithic biofilms affected by acid-mine drainage

Sarah Zecchin N. Guerrieri Evelien Jongepier Leonardo Scaglioni Gigliola Borgonovo

Arsenic is a toxic but naturally abundant metalloid that globally leads to contamination in groundwater and soil, exposing millions of people to cancer and other arsenic-related diseases. In several areas in Northern Italy arsenic in soil and water exceeds law limits (20 mg kg-1 and 10 mg L-1, respectively), due to both the mineralogy of bedrock and former mining activities. The Rio Rosso stream, located in the Anzasca Valley (Piedmont) is heavily affected by an acid mine drainage originated from an abandoned gold mine. Arsenic, together with other heavy metals, is transferred by the stream to the surrounding area. The stream is characterized by the presence of an extensive reddish epilithic biofilm at the opening of the mine and on the whole contaminated waterbed. The aim of this study was to characterize the mechanisms allowing the biotic fraction of this biofilm to cope with extreme arsenic concentrations. The composition and functionality of the microbial communities constituting the epilithic biofilms sampled in the close proximity and downstream the mine were unraveled by 16S rRNA genes and shotgun Illumina sequencing in relation to the extreme physico-chemical parameters. In parallel, autotrophic and heterotrophic microbial populations were characterized in vivo by enrichment cultivation and isolated strains were tested for their ability to perform arsenic redox transformation. Preliminary analyses indicated that the biofilm accumulated arsenic in the order of 6 &#183; 103 mg kg-1, in contrast to 0.14 mg L-1, measured in the surrounding water. The main chemical parameter affecting the composition of the microbial community was the pH, being 2 next to the mine and 6.7 in the downstream sampling point. In both sampling sites iron- and sulfur-cycling microorganisms were retrieved by both cultivation and molecular methods. However, the diversity of the microbial community living next to the mine was significantly lower with respect to the community developed downstream. In the latter, autotrophic Cyanobacteria belonging to the species Tychonema were the dominant taxa. A complete arsenic cycle was shown to occur, with heterotrophic bacteria mainly responsible for arsenate reduction and autotrophic bacteria performing arsenite &#160;oxidation. These observations indicate that the epilithic biofilm living in the Rio Rosso stream represents a peculiar ecosystem where microorganisms cope with metalloid toxicity likely using diverse mechanisms. Such microbial metabolic properties might be exploited in bioremediation strategies applied in arsenic-contaminated environments.

Acid Mine Drainage

Metalloid

10.5194/biofilms9-81

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Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway

Frontiers in Microbiology (2019)

Anne-Catherine Ahn Lucia Cavalca Milena Colombo J. Merijn Schuurmans Dimitry Y. Sorokin

The genus Thioalkalivibrio includes haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria isolated from various soda lakes worldwide. Some of these lakes possess in addition to their extreme haloalkaline environment also other harsh conditions, to which Thioalkalivibrio needs to adapt. An example is arsenic in soda lakes in eastern California, which is found there in concentrations up to 3000 µM. Arsenic is a widespread element that can be an environmental issue, as it is highly toxic to most organisms. However, resistance mechanisms in the form of detoxification are widespread and some prokaryotes can even use arsenic as an energy source. We first screened the genomes of 76 Thioalkalivibrio strains for the presence of known arsenic oxidoreductases and found 15 putative ArxA (arsenite oxidase) and two putative ArrA (arsenate reductase). Subsequently, we studied the resistance to arsenite in detail in Tv. jannaschii ALM2T and Tv. thiocyanoxidans ARh2T by comparative genomics and by growing them at different arsenite concentrations followed by arsenic species and transcriptomic analysis. Tv. jannaschii ALM2T, which has been isolated from Mono Lake, an arsenic-rich soda lake, could resist up to 5 mM arsenite, whereas Tv. thiocyanoxidans ARh2T, which was isolated from a Kenyan soda lake, could only grow up to 0.1 mM arsenite. Interestingly, both species oxidized arsenite to arsenate under aerobic conditions, although Tv. thiocyanoxidans ARh2T does not contain any known arsenite oxidase, and in Tv. jannaschii ALM2T, only arxB2 was clearly upregulated. However, we found the expression of a SoeABC-like gene, which we assume might have been involved in arsenite oxidation. Other arsenite stress responses for both strains were the upregulation of the vitamin B12 synthesis pathway, which can be linked to antioxidant activity, and the up- and downregulation of different DsrE/F-like genes whose roles are still unclear. Moreover, Tv. jannaschii ALM2T induced the ars gene operon and the Pst system, and Tv. thiocyanoxidans ARh2T upregulated the sox and apr genes as well as different heat shock proteins. Our findings for Thioalkalivibrio confirm previously observed adaptations to arsenic, but also provide new insights into the arsenic stress response and the connection between the arsenic and the sulfur cycle.

10.3389/fmicb.2019.01514

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Anaerobic and aerobic bioremediation of chlorinated solvents and hydrocarbons plumes from an old landfill in the Venice lagoon environment

Gabriele Beretta Lucia Cavalca M. Bertolini Sarah Zecchin Bernardini Giovanni

Chlorinated solvents

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Microbial transformations of arsenic: perspectives for biological removal of arsenic from water

Future Microbiology (2013)

Lucia Cavalca A. Corsini P. Zaccheo V. Andreoni Gerard Muyzer

Arsenic is present in many environments and is released by various natural processes and anthropogenic actions. Although arsenic is recognized to cause a wide range of adverse health effects in humans, diverse bacteria can metabolize it by detoxification and energy conservation reactions. This review highlights the current understanding of the ecology, biochemistry and genomics of these bacteria, and their potential application in the treatment of arsenic-polluted water.

Detoxification

10.2217/fmb.13.38

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Citations (105)

Influence of microorganisms on arsenic mobilization and speciation in a submerged contaminated soil: Effects of citrate

Applied Soil Ecology (2011)

A. Corsini Lucia Cavalca P. Zaccheo L. Crippa V. Andreoni

Geobacter

10.1016/j.apsoil.2011.06.010

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Citations (18)

Rice Paddy Nitrospirae Carry and Express Genes Related to Sulfate Respiration: Proposal of the New Genus “Candidatus Sulfobium”

Applied and Environmental Microbiology (2017)

Sarah Zecchin Ralf Mueller Jana Seifert Ulrich Stingl Karthik Anantharaman

Nitrospirae spp. distantly related to thermophilic, sulfate-reducing Thermodesulfovibrio species are regularly observed in environmental surveys of anoxic marine and freshwater habitats. Here we present a metaproteogenomic analysis of Nitrospirae bacterium Nbg-4 as a representative of this clade. Its genome was assembled from replicated metagenomes of rice paddy soil that was used to grow rice in the presence and absence of gypsum (CaSO4·2H2O). Nbg-4 encoded the full pathway of dissimilatory sulfate reduction and showed expression of this pathway in gypsum-amended anoxic bulk soil as revealed by parallel metaproteomics. In addition, Nbg-4 encoded the full pathway of dissimilatory nitrate reduction to ammonia (DNRA), with expression of its first step being detected in bulk soil without gypsum amendment. The relative abundances of Nbg-4 were similar under both treatments, indicating that Nbg-4 maintained stable populations while shifting its energy metabolism. Whether Nbg-4 is a strict sulfate reducer or can couple sulfur oxidation to DNRA by operating the pathway of dissimilatory sulfate reduction in reverse could not be resolved. Further genome reconstruction revealed the potential to utilize butyrate, formate, H2, or acetate as an electron donor; the Wood-Ljungdahl pathway was expressed under both treatments. Comparison to publicly available Nitrospirae genome bins revealed the pathway for dissimilatory sulfate reduction also in related Nitrospirae recovered from groundwater. Subsequent phylogenomics showed that such microorganisms form a novel genus within the Nitrospirae, with Nbg-4 as a representative species. Based on the widespread occurrence of this novel genus, we propose for Nbg-4 the name "Candidatus Sulfobium mesophilum," gen. nov., sp. nov.IMPORTANCE Rice paddies are indispensable for the food supply but are a major source of the greenhouse gas methane. If it were not counterbalanced by cryptic sulfur cycling, methane emission from rice paddy fields would be even higher. However, the microorganisms involved in this sulfur cycling are little understood. By using an environmental systems biology approach with Italian rice paddy soil, we could retrieve the population genome of a novel member of the phylum Nitrospirae This microorganism encoded the full pathway of dissimilatory sulfate reduction and expressed it in anoxic paddy soil under sulfate-enriched conditions. Phylogenomics and comparison to the results of environmental surveys showed that such microorganisms are actually widespread in freshwater and marine environments. At the same time, they represent an undiscovered genus within the little-explored phylum Nitrospirae Our results will be important for the design of enrichment strategies and postgenomic studies to further understanding of the contribution of these novel Nitrospirae spp. to the global sulfur cycle.

Candidatus

10.1128/aem.02224-17

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Citations (85)