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Geomicrobiology of Parys mine, Wales: Influence of mineralogy on the development, composition and functioning of microbial communities

Final Report Summary - PARMIN (Geomicrobiology of Parys mine, Wales: Influence of mineralogy on the development, composition and functioning of microbial communities)

A growing body of scientific evidence, particularly within the last decade, suggests that the chemical composition of rocks, i.e. their mineralogy, plays a key role in shaping the structure of the inhabiting microbial communities. Much of this work was done on soil minerals [1-2], and on minerals of volcanic origin such as lava deposits, both terrestrial [3-4] and marine [5]. Until the PARMIN (PARys MINerals) project however, no study had considered the potential effects of mineralogy on the structure of mineral-associated microbial communities in an acid mine environment. A likely reason for this perhaps is that such environments are considered extreme in terms of microbial life, with limited organic compounds, extreme acidity, and often high concentrations of elements such as copper and lead (among others), which can prove toxic to microbial life. Microbiologically-orientated studies of such environments to date, while not focusing on mineralogical differences, have revealed the presence of what can be termed ‘cosmopolitan’ microbial taxa (at the level of genus), found in various acid mine environments all over the world. Examples of these include the bacterial genera Leptospirillum, Acidithiobacillus, Ferrovum and Acidiphilium. Among the archaea, a large group of microorganisms, which superficially often look like bacteria but are genetically and physiologically very distinct, Ferroplasma is among the most common genera detected. These and other common genera in such extreme acidic environments are adapted to and prefer the acidic conditions, resulting in their classification as acidophiles. In a given acid mine system, samples tend to be dominated by one or a handful of these or similar genera of bacteria and archaea acidophiles, and contain relatively few species of microorganisms overall.

In order to address the important outstanding scientific question of the effect of mineralogy on microbial community composition, PARMIN research focused on minerals found within the subterranean workings of the disused copper mine at Parys Mountain (Mynydd Parys) in north Wales (UK), once the largest supplier of copper in the world ( Mynydd Parys is representative of many similar abandoned copper mines in the UK and further afield.

The specific objectives of the project were to: 1) characterise the structure of established microbial (bacteria and archaea only) communities inhabiting a range of minerals 2) monitor the development of microbial communities on two primary minerals (chalcopyrite and sphalerite) 3) determine the activities of microbial communities on these two minerals 4) isolate Archaea in pure culture from Mynydd Parys.

The final conclusions of this project are:
- Even within such an extreme acidic environment, mineral chemistry has an influence on the structure of microbial communities.
- The diversity of bacteria genera residing in the minerals is greater than expected, and there is a larger range of bacteria genera present per sample than anticipated.
- Typical genera usually associated with acid mines often do not dominate (in terms of abundance) in microbial communities within mineral samples in Mynydd Parys, however typical acid mine genera such as Leptospirillum and Acidithiobacillus do dominate the water samples in the mine.
- Genera not previously associated with acid mine communities are present in Mynydd Parys, one of which was isolated from mineral samples in pure culture (three separate isolates) on growth media specific for acid-loving microorganisms
- A new species of Sulfobacillus, a genus of bacteria common in acid mine systems, was isolated and, initial testing suggests it behaves differently to known Sulfobacillus species. Future analyses will reveal whether it may have any biotechnological uses.
- Diversity of archaea within the mine is low, and the proportion of archaea in a mineral community was generally low (<10% of the community).
- The low abundance of archaea compared to bacteria in the samples, resulted in a dominance of bacteria in enrichment cultures. Such competition, possibly in combination with unsuitable laboratory conditions for the unknown archaea, resulted in the failure to achieve pure-cultures of archaea by established and modified laboratory methods. The inability to culture the majority of environmental microbes is a recognised phenomenon in microbiology (i.e. “the great plate count anomaly”)
- Within Mynydd Parys, a vast array of mineral and other novel samples were examined as part of the study. Amongst these samples were two minerals not previously recorded in Wales (aluminite and boothite)
- Overall, the results of this study indicate previous studies focusing on water samples within acid mine environments, including Mynydd Parys, have only provided a glimpse into the microbial diversity which may be present in such environments. Not only do such mineral environments host unexpectedly high diversity communities, but novel microbes. Furthermore, despite the extreme external environmental conditions, namely extreme acidic pH, the structure of acid mine mineral communities are greatly influenced by the elemental composition of the mineral on which they live.

Project resources: a webpage dedicated to the PARMIN project is hosted on the Researchers personal webpage and will continue to be updated with detailed data, following their publication in scientific outlets. The page is accessible at the following address:

References: [1] Certini, G., Campbell, C.D. & Edwards, A.C. Soil Biol. Biochem. 36, 1119-1128 (2004) [2] Carson, J.K. et al. FEMS Microbiol. Ecol. 67, 381-388 (2009). [3] Kelly, L.C. et al. Microb. Ecol. 62, 69-79 (2011) [4] Kelly, L.C. et al. Microb. Ecol. 60, 740-752 (2010) [5] Mason, O.U. et al. Environ. Microbiol. 9, 2539-2550 (2007).