Hydrogen is a key energy source for subsurface microbial processes, particularly in subsurface environments with limited alternative electron donors, and environments that are not well connected to the surface. In addition to consumption of hydrogen, microbial processes such as fermentation and nitrogen fixation produce hydrogen. Hydrogen is also produced by a number of abiotic processes including radiolysis, serpentinization, graphitization, and cataclasis of silicate minerals. Both biotic and abiotically generated hydrogen may become available for consumption by microorganisms, but biotic production and consumption are usually tightly coupled. Understanding the microbiology of hydrogen cycling is relevant to subsurface engineered environments where hydrogen-cycling microorganisms are implicated in gas consumption and production and corrosion in a number of industries including carbon capture and storage, energy gas storage, and radioactive waste disposal. The same hydrogen-cycling microorganisms and processes are important in natural sites with elevated hydrogen and can provide insights into early life on Earth and life on other planets. This review draws together what is known about microbiology in natural environments with elevated hydrogen, and highlights where similar microbial populations could be of relevance to subsurface industry.

Aims: The objective of the work was to determine whether known strains of nonpathogenic vibrios can act as probiotics for the control of Vibrio infections in the Pacific white shrimp, Litopenaeus vannamei. Methods and Results: Of the ten species tested, only Vibrio alginolyticus (NCIMB 1339) and Vibrio gazogenes (NCIMB 2250) showed antagonistic activity towards a panel of shrimp pathogenic vibrios. In the case of V. alginolyticus, this activity depended on the presence of live bacteria while in V. gazogenes both live and dead bacteria showed anti‐Vibrio activity. Injection of shrimp with either V. alginolyticus or V. gazogenes at 3 × 10⁷ or 3 × 10⁵ total bacteria per shrimp resulted in mortality with higher levels in the case of V. alginolyticus (100% mortality 18 h postinjection of 3 × 10⁷ bacteria). Juvenile shrimp were fed commercial diets top‐coated with either chitin (an immune stimulant) or chitin + V. gazogenes. Both chitin and V. gazogenes caused a significant decline in the number of Vibrio‐like bacteria in the fore and hind gut, and changes were also seen in the hepatosomatic index (a measure of digestive health) and the total number of blood cells in circulation. Analysis of mid/hindgut and faecal samples obtained using terminal restriction fragment length polymorphism showed that the gut microbiota of shrimp has limited bacterial diversity and that after 8 weeks exposure to the experimental diets there were significant changes in the microbial flora of the GI tract of shrimp as a result of the presence of V. gazogenes. Conclusions: Of the vibrios tested, V. gazogenes has potential as a probiotic for the control of bacterial diseases in shrimp. Significance and Impact of the Study: Overall, this study shows the promise of V. gazogenes together with chitin to improve the health and welfare of shrimp under aquaculture conditions.

Rare earth elements (REE) are considered to be a critical resource, because of their importance in green energy applications and the overdependence on Chinese imports. REE rich ion-adsorption deposits (IAD) result from tropical weathering of REE enriched igneous rocks. Commercial REE leaching from IAD, using salt solutions occurs via an ion-exchange mechanism. Bioleaching of IAD by Aspergillus or Bacillus, was compared to Uninoculated Control and Salt leaching (0.5 M ammonium sulfate) over 60 days. Salt leaching was most effective, followed by Aspergillus, Bacillus then Uninoculated Control. Most of the REE and major elements released by Salt leaching occurred before day 3. With bioleaching, REE and major elements release increased with time and had a greater heavy to light REE ratio. Similar total heavy REE release was observed in Salt leaching and Aspergillus (73.1% and 70.7% Lu respectively). In bioleaching experiments, pH was inversely correlated with REE release (R² = 0.947 for Lu) indicating leaching by microbially produced acids. These experiments show the potential for bioleaching of REE from IAD, but dissolution of undesirable elements could cause problems in downstream processing. Further understanding of the bioleaching mechanisms could lead to optimization of REE recovery.

Several rickettsia-like diseases have been reported in arthropods (insects and crustaceans), some of which result in significant losses of economically important species such as shrimp and crabs. This study reports on the molecular pathology of a recently emerged disease of the European shore crab, Carcinus maenas, termed milky disease – named as a result of the unusual milky appearance of the haemolymph (blood). This disease was more prevalent (>26 %) during summer months when the water temperature in a pilot crab farm was approximately 19 °C. The putative causative agent of the disease was a Gram-negative bacterium that could not be cultured on a range of agar-based growth media. Diseased crabs showed significant reductions in free blood cell numbers and total serum protein. Such animals also displayed raised levels of glucose and ammonium in blood. Ultrastructural and in situ hybridization studies revealed that the causative agent associated with milky disease multiplied in the fixed phagocytes of the hepatopancreas (digestive gland), ultimately to be released into the haemolymph, where the circulating blood cells showed little response to the presence of these agents. Attempts to induce the infection by short-term temperature stress failed, as did transmission experiments where healthy crabs were fed infected tissues from milky disease affected individuals. Sequence analysis of the 16S rRNA gene from the milky disease bacteria indicated that they are a previously undescribed species of α-proteobacteria with little phylogenetic similarity to members of the order Rickettsiales.

Approximately 300 million tonnes of bauxite are processed annually, primarily to extract alumina, and can contain moderate rare earth element (REE) concentrations, which are critical to a green energy future. Three bioleaching techniques (organic acid, reductive and oxidative) were tested on three karst bauxites using either Aspergillus sp. (organic acid bioleaching) or Acidithiobacillus ferrooxidans (reductive and oxidative bioleaching). Recovery was highest in relation to middle REE (generally Nd to Gd), with maximum recovery of individual REE between 26.2% and 62.8%, depending on the bauxite sample. REE recovery occurred at low pH (generally < 3), as a result of organic acids produced by Aspergillus sp. or sulphuric acid present in A. ferrooxidans growth media. Acid production was seen when A. ferrooxidans was present. However, a clear increase in REE recovery in the presence of A. ferrooxidans (compared to the control) was only seen with one bauxite sample (clay-rich) and only under oxidative conditions. The complex and varied nature of REE-bearing minerals in bauxite provides multiple targets for bioleaching, and although the majority of recoverable REE can be leached by organic and inorganic acids, there is potential for enhanced recovery by bioleaching.