Microbial populations in acid mineral bioleaching systems of Tong Shankou Copper Mine, China

Leptospirillum spp. are widespread members of acidophilic microbial communities that catalyze ferrous iron oxidation, thereby increasing sulfide mineral dissolution rates. These bacteria play important roles in environmental acidification and are harnessed for bioleaching-based metal recovery. Known members of the Leptospirillum clade of the Nitrospira phylum are Leptospirillum ferrooxidans (group I), Leptospirillum ferriphilum and "Leptospirillum rubarum" (group II), and Leptospirillum ferrodiazotrophum (group III). In the Richmond Mine acid mine drainage (AMD) system, biofilm formation is initiated by L. rubarum; L. ferrodiazotrophum appears in later developmental stages. Here we used community metagenomic data from unusual, thick floating biofilms to identify distinguishing metabolic traits in a rare and uncultivated community member, the new species "Leptospirillum group IV UBA BS." These biofilms typically also contain a variety of Archaea, Actinobacteria, and a few other Leptospirillum spp. The Leptospirillum group IV UBA BS species shares 98% 16S rRNA sequence identity and 70% average amino acid identity between orthologs with its closest relative, L. ferrodiazotrophum. The presence of nitrogen fixation and reverse tricarboxylic acid (TCA) cycle proteins suggest an autotrophic metabolism similar to that of L. ferrodiazotrophum, while hydrogenase proteins suggest anaerobic metabolism. Community transcriptomic and proteomic analyses demonstrate expression of a multicopper oxidase unique to this species, as well as hydrogenases and core metabolic genes. Results suggest that the Leptospirillum group IV UBA BS species might play important roles in carbon fixation, nitrogen fixation, hydrogen metabolism, and iron oxidation in some acidic environments.

mentioning

confidence: 99%

New Group in the Leptospirillum Clade: Cultivation-Independent Community Genomics, Proteomics, and Transcriptomics of the New Species “Leptospirillum Group IV UBA BS”

Goltsman

Dasari

Thomas

et al. 2013

“…Acidophilic Leptospirillum bacteria dominate this AMD system (15), other AMD systems (54), and bioleaching systems used for recovery of metals (19,53,86). These bacteria play pivotal roles in sulfide mineral dissolution because they are iron oxidizers (53,75), and ferric iron drives sulfide oxidation, leading to formation of metal-rich sulfuric acid solutions.…”

mentioning

confidence: 99%

Community Genomic and Proteomic Analyses of Chemoautotrophic Iron-Oxidizing “ Leptospirillum rubarum ” (Group II) and “ Leptospirillum ferrodiazotrophum ” (Group III) Bacteria in Acid Mine Drainage Biofilms

Goltsman

Denef

Singer

et al. 2009

163

153

We analyzed near-complete population (composite) genomic sequences for coexisting acidophilic ironoxidizing Leptospirillum group II and III bacteria (phylum Nitrospirae) and an extrachromosomal plasmid from a Richmond Mine, Iron Mountain, CA, acid mine drainage biofilm. Community proteomic analysis of the genomically characterized sample and two other biofilms identified 64.6% and 44.9% of the predicted proteins of Leptospirillum groups II and III, respectively, and 20% of the predicted plasmid proteins. The bacteria share 92% 16S rRNA gene sequence identity and >60% of their genes, including integrated plasmid-like regions. The extrachromosomal plasmid carries conjugation genes with detectable sequence similarity to genes in the integrated conjugative plasmid, but only those on the extrachromosomal element were identified by proteomics. Both bacterial groups have genes for community-essential functions, including carbon fixation and biosynthesis of vitamins, fatty acids, and biopolymers (including cellulose); proteomic analyses reveal these activities. Both Leptospirillum types have multiple pathways for osmotic protection. Although both are motile, signal transduction and methyl-accepting chemotaxis proteins are more abundant in Leptospirillum group III, consistent with its distribution in gradients within biofilms. Interestingly, Leptospirillum group II uses a methyldependent and Leptospirillum group III a methyl-independent response pathway. Although only Leptospirillum group III can fix nitrogen, these proteins were not identified by proteomics. The abundances of core proteins are similar in all communities, but the abundance levels of unique and shared proteins of unknown function vary. Some proteins unique to one organism were highly expressed and may be key to the functional and ecological differentiation of Leptospirillum groups II and III.To understand how microorganisms contribute to biogeochemical cycling, it is necessary to determine the roles of uncultivated as well as cultivated groups and to establish how these roles vary during ecological succession and when environmental conditions change. Shotgun genomic sequencing (metagenomics) has opened new opportunities for cultureindependent studies of microbial communities. Examples include investigations of acid mine drainage (AMD) biofilm communities (4, 43, 75), symbiosis in a marine worm involving sulfur-oxidizing and sulfate-reducing bacteria (85), and enhanced biological phosphorous removal by sludge communities (32). From these genomic data sets, it has been possible to reconstruct aspects of the metabolism of individual organisms (32) and coexisting community members (29, 75) and to identify which organisms contribute community-essential functions (75). An interesting question relates to how differences in metabolic potential between organisms from the same lineage allow them to occupy distinct niches. Identification of potentially adaptive traits in closely related organisms is also important from an evolutionary perspective.Genomic data do not...

“…Detection or quantification of the Ferroplasmaceae in these environments was done mostly using small subunit (SSU) rRNA-targeting analyses, such as 16S rRNA gene clone libraries' sequencing, amplified rRNA gene restriction analysis (ARDRA) profiling, real-time quantitative PCR, restriction fragment length polymorphism (RFLP) or fluorescence in situ hybridization (FISH), and oligonucleotide microarray analysis, all of which revealed the presence of these archaea in a number of pyritic/arsenopyritic, gold-arsenopyritic/chalcopyritic, and lead-, zinc-, and copper-containing mines across all continents (11,24,26,45,46,51,55,56,57,58). Clones related to the family Ferroplasmaceae have also been documented in further natural sulfide-rich ecosystems, e.g., in the snottites, i.e., the stalactite-like formations of microbial origin taken from the walls of Frasassi Cave and in the Rio Garrafo cave systems, both located in Italy, where acidic microenvironments were formed as a result of sulfide oxidation (38).…”

mentioning

confidence: 99%

Environmental, Biogeographic, and Biochemical Patterns of Archaea of the Family Ferroplasmaceae

Golyshina

2011

About 10 years ago, a new family of cell wall-deficient, iron-oxidizing archaea, Ferroplasmaceae, within the large archaeal phylum Euryarchaeota, was described. In this minireview, I summarize the research progress achieved since then and report on the current status of taxonomy, biogeography, physiological diversity, biochemistry, and other research areas involving this exciting group of acidophilic archaea.Microorganisms thrive remarkably under various conditions, including high temperatures, extremely high osmosis, and very acidic pH, that would generally be considered hostile or limiting to higher organisms. Studying and understanding the uniqueness of extremophilic organisms and the biochemical and cellular processes underlying their functioning and role in biogeochemical processes comprise an emerging research area in modern bioscience. Of special interest for various biotechnological applications are enzymes produced by extremophiles, the so-called extremozymes, which exhibit a high activity and stability under extreme physical-chemical conditions. The representatives of the "third domain of life," the archaea, are unique contributors to this area of special interest. Several factors make the archaea an attractive subject of study, including their relatively recent history of discovery, ability (often much higher than that of bacteria) to adapt to harsh environments, enigmatic nature, and low cultivability.