Distributional, metagenomic and geochemical insights into ecophysiology and niche differentiation in communities of the giant sulphur oxidising bacteria from the genus Achromatium

Overview

The family Achromatiaceae are conspicuous (giant), single-celled, freshwater bacteria within the Gammaproteobacteria. Know since the 19th century they have yet to be laboratory grown though past ecophysiological and genetic studies suggest energy and growth from sulfide oxidation. Globally distributed [1], at local scales, Achromatium (as multiple coexisting species) are present in large numbers occasionally accounting for approximately 90 % of the sediment bacterial bio-volume [ 2, 3, 4]. Despite a flurry of recent papers e.g. [5, 6, 7] including those that have revealed some extraordinary structural and genomic insights, there are many questions that remain to be answered about their diversity, distribution, function and geochemical impact. For instance, in there is, as yet, no settled consensus [1, 5] on the physiological reason that this family uniquely within the entire bacterial domain precipitates intracellular calcium carbonate in the form of calcite (figure 1).

Taking advantage of molecular genetic (i.e. next generation DNA and RNA sequencing and sophisticated analysis pipelines) and geochemical (including stable isotope geochemistry) tools not available in previous studies, this project will focus on determining the impact that Achromatium communities have on geochemical environments and identify interactions with the sediment microbiome in sites in the English Lake district. From a geochemical perspective Achromatium represents an ideal model system to understand drivers of microbial diversity with a specific focus on the role of depth related diffusional controlled redox successions which occur in sediments. From such multidisciplinary work it should be possible to more clearly understand this unique bacterial lineage and its interaction with the sedimentary carbon, nitrogen and sulphur cycles.

The key objectives of a project will be:

1. to derive and analyse genomes (from single cells) or metagenomes (from physically purified preparations) of multiple coexisting Achromatium species to resolve functional variation within communities.

2. to relate different depth distributions of individual Achromatium species to a full analysis of the microbial diversity and function in the system (16S rRNA community analysis) and inferred metagenomics. Such fine scale depth related microbial community profiling is a useful geochemical proxy for Eh gradient reconstruction indicative of transitions from aerobic to anaerobic processes. The advantage of a DNA based approach is the identification of coupled/cryptic geochemical processes missed with ‘snap shot’ geochemical measurements and longer term time-integrated assessments of redox gradients. Such a finely constrained geochemical and biological context should be relatable to Achromatium genetic variations (see objective 1).

3. to relate community variation with a comprehensive geochemical analysis of solid phases and pore waters to be linked to thermodynamic geochemical outcome, namely, mineral saturation indices at different depths. Such outputs will predict/infer relevant properties of sediments such as maximal free sulphide concentrations (if not measurable directly in pore waters) and the thermodynamic constraints on calcification at different depths – A critical question – is Achromatium swimming metaphorically with or against the thermodynamic tide with respect to calcification?

4. to carry out a comprehensive analysis of the sedimentary sulphur isotopes including for Achromatium’s intracellular sulphur. We hypothesis that a greater proportion of sedimentary carbon is turned over via sulphur cycling in these low sulphur sediments because of efficient re-oxidation mediated even under conditions where free sulphide is further limited due to high dissolved iron concentrations.

5. to evaluate geochemical and molecular genetic data with specific geographical and geological characteristics in the context of other Achromatium studies elsewhere to identify similarities and dissimilarities indicative of core family ecophysiologies and species adaptations.

Click on an image to expand

Image Captions

Figure 1. Scanning electron micrographs of Achromatium cells from Rydal Water, Cumbria, UK. Top panel: intact elongated cell. Bottom panel: an elongated cell disrupted by grinding in a pestle and mortar showing larger calcite inclusions and smaller sulfur inclusions. Scale bars 20µM

Methodology

The project will involve:

1. field based sampling including physical separation/isolation of Achromatium communities for DNA/RNA extraction and preservation.

2. chemical analysis including sediment elemental profiling (by digestion and ICP-OES) and analysis of pore water for cations and anions. Geochemical modelling will be conducted on data (Geochemists Workbench, Phreeqc)

3. production of genomes/metagenomes and 16S rRNA sequence libraries (Next generation sequencing) from single cells, Achromtium cell pellet purifications, and total sediment DNA extractions followed be processing in bioinformatics analysis pipelines

4. Sulfur isotope analysis (at St Andrews under the guidance of Dr Zerkle) with a unique capability (UK) for the measurement of 32S, 34S, 33S and 36S which is required for unravelling complex sulfur cycling in such sedimentary environments where oxidative S cycling metabolisms have very small fractionations in d34S.

Project Timeline

Year 1

Project proposal development via extensive literature review. Training in molecular tools and Achromatium specific techniques. Sediment sampling and processing for chemical and microbiological analysis

Year 2

Geochemical and DNA sequence datasets analysis, Modelling and sulfur isotope work, scientific papers

Year 3

Synthesis of different information streams to address core project hypotheses. Thesis preparation

Year 3.5

Thesis completion and paper writing

Training
& Skills

The host, Newcastle’s Geomicrobiology group (supervised by Gray and Head) is part of the Earth, Ocean and Planetary Science research group so, in addition, to our research interests in mineral-microbe interactions, the student will have access to a wider range of Earth Science expertise e.g. MSc course modules including block taught Research methods, inorganic and organic analytical chemistry, geochemical modelling and environmental microbiology. The student will receive training in stable isotope geochemistry in the Zerkle lab.

This project involves substantial laboratory work including state-of-the-art geochemical and microbiological techniques, as well as quantitative skills in interpreting geochemical data and setting up and running bioinformatics pipelines. The student will acquire general skills such as critical thinking, oral and written science communication, through manuscript preparation and presentation of work at scientific conferences.

References & further reading

[1] Gray ND & Head IM, in The Prokaryotes 1-14 (Springer Berlin Heidelberg, (2014)[2] Gray ND et al. Env Microbiol 6, 669-677 (2004)[3] Gray ND et al. Appl Environ Microbiol 66, 4518-4522 (2000)[4] Head IM et al. Microbiology 142, 2341-2354 (1996)[5] Ionescu D et al. Nat Commun 8, 455 (2017)[6] Mansor, M et al. Front Microbiol 6, 822 (2015)[7] Salman, V et al. ISME J. 9, 2503-2514 (2015)

Further Information

For further information please contact Dr Neil Gray (neil.gray@newcastle.ac.uk) or Dr Aubrey Zerkle (az29@st-andrews.ac.uk)

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