Microphytobenthic extracellular polymeric substances (EPS) in intertidal sediments fuel both generalist and specialist EPS-degrading bacteria

Microphytobenthic biofilms contain high concentrations of carbohydrate-rich extracellular polymeric substances (EPS) that are important in sediment carbon cycling. Field measurements at two locations in the Colne Estuary, U.K., showed that a significant curvilinear relationship explained 50% of the variability in chlorophyll a and EPS content. Estimates of EPS production, based on field data and published rates of production by diatoms, revealed that EPS turnover of 52% to 369% over the tidal cycle was required to account for field standing stocks. We investigated EPS degradation in sediment slurries using purified 13C-EPS produced by the diatom Nitzschia tubicola. Although EPS constituted only 5% of the sediment dissolved organic carbon (DOC) pool, 100% of the added EPS was utilized within 30 h, before decreases in other sediment-carbohydrate fractions and DOC concentrations. A general 13C enrichment of phospholipid fatty acids (PLFAs), representative of Gram-positive and Gram-negative bacteria, occurred within 6 h, with the PLFAs a15:0, i15:0, and 18:1?7c being highly enriched. The diatom PLFA 20:5?3 had relatively low but significant 13C enrichment. Stable isotope probing of 16S ribosomal ribonucleic acid (RNA-SIP) at 30 h revealed 13C-enriched sequences from the diatom genus Navicula; further evidence that diatoms assimilated the EPS, or EPS-breakdown products, from other diatom taxa. RNA-SIP also demonstrated a diverse range of highly 13C-enriched bacterial taxa, including a distinct subset (Alphaproteobacteria and Gammaproteobacteria) found only in the heavily labeled microbial assemblages. Thus, cycling of diatom EPS is rapid, and involves a wide range of microbial taxa, including some apparent specialists

Marine crude-oil biodegradation: a central role for interspecies interactions

The marine environment is highly susceptible to pollution by petroleum, and so it is important to understand how microorganisms degrade hydrocarbons, and thereby mitigate ecosystem damage. Our understanding about the ecology, physiology, biochemistry and genetics of oil-degrading bacteria and fungi has increased greatly in recent decades; however, individual populations of microbes do not function alone in nature. The diverse array of hydrocarbons present in crude oil requires resource partitioning by microbial populations, and microbial modification of oil components and the surrounding environment will lead to temporal succession. But even when just one type of hydrocarbon is present, a network of direct and indirect interactions within and between species is observed. In this review we consider competition for resources, but focus on some of the key cooperative interactions: consumption of metabolites, biosurfactant production, provision of oxygen and fixed nitrogen. The emphasis is largely on aerobic processes, and especially interactions between bacteria, fungi and microalgae. The self-construction of a functioning community is central to microbial success, and learning how such " microbial modules" interact will be pivotal to enhancing biotechnological processes, including the bioremediation of hydrocarbons. © 2012 McGenity et al.; licensee BioMed Central Ltd

Biofilm and planktonic bacterial and fungal communities transforming high molecular weight polycyclic aromatic hydrocarbons.

High molecular weight polycyclic aromatic hydrocarbons (HMW-PAHs) are natural components of fossil fuels that are carcinogenic and persistent in the environment, particularly in oil sands process-affected water (OSPW). Their hydrophobicity and tendency to adsorb to organic matter result in low bioavailability and high recalcitrance to degradation. Despite the importance of microbes for environmental remediation, little is known about those involved in HMW-PAH transformations. Here, we investigated the transformation of HMW-PAHs using samples of OSPW, and compared the bacterial and fungal community composition attached to hydrophobic filters and in suspension. It was anticipated that the hydrophobic filters with sorbed HMW-PAHs would select for microbes that specialise in adhesion. Over 33 days more pyrene was removed (75% ± 11.7) than the five-ring PAHs benzo[a]pyrene (44% ± 13.6) and benzo[b]fluoranthene (41% ± 12.6). For both bacteria and fungi, the addition of PAHs led to a shift in community composition, but thereafter the major factor determining the fungal community composition was whether they were in the planktonic phase or attached to filters. In contrast, the major determinant of the bacterial community composition was the nature of the PAH serving as the carbon source. The main bacteria enriched by HMW-PAHs were Pseudomonas, Bacillus and Microbacterium species. This report demonstrates that OSPW harbour microbial communities with the capacity to transform HMW-PAHs. Furthermore, the provision of suitable surfaces that encourage PAH sorption and microbial adhesion select for different fungal and bacterial species with the potential for HMW-PAH degradation

Mars simulated exposure and the characteristic Raman biosignatures of amino acids and halophilic microbes

Though Raman bands of α-amino acids (AA) are well documented, often only the strongest intensity bands are quoted as identifiers (e.g. Jenkins et al., 2005; De Gelder et al., 2007; Zhu et al., 2011). Unknown regolith mixtures on Mars-sampling missions could obscure these bands. Here the case is made for determining, via a statistical method, sets of characteristic bands to be used as identifiers, independent of band intensity or number of bands (Rolfe et al., 2016). AA have upwards of 25 potentially identifying bands and this method defines sets of 10–19 bands per AA. Examination of AA-doped Mars-like basalt resulted in a maximum of eight bands being identified, as some characteristic bands were obscured by mineral bands, including the strongest intensity band in some cases. This proved the need for characteristic bands to be defined, enabling successful identification of AA. The ESA ExoMars Rover mission will crush and then pass the sample to the Raman Laser Spectrometer. We crushed a Mars-like basalt to a similar grain size expected to be created by the rover. Our samples were doped with 1 % (by weight) AA samples, resulting in no detection of AA, because of loss of original spatial context and spaces between the grains. We recommend that Raman spectroscopy on future missions should be conducted before the sample is crushed. Halite-entombed halophilic microbes, known to survive being entombed, were exposed to Mars-like surface (including temperature, pressure, atmospheric composition and UV) and freeze-thaw cycle (plus pressure and atmospheric composition) conditions. This test on the survival of the microbes showed that survival rates quickly deteriorated in surface conditions, but freeze-thaw cycle samples had well preserved Raman biosignatures, indicating that similar signatures could be detectable on Mars if similar life persists in evaporitic material or brines today

Molecular ecology of isoprene-degrading bacteria

Isoprene is a highly abundant biogenic volatile organic compound (BVOC) that is emitted to the atmosphere in amounts approximating to those of methane. The effects that isoprene has on Earth’s climate are both significant and complex, however, unlike methane, very little is known about the biological degradation of this environmentally important trace gas. Here, we review the mechanisms by which bacteria catabolise isoprene, what is known about the diversity of isoprene degraders in the environment, and the molecular tools currently available to study their ecology. Specifically, we focus on the use of probes based on the gene encoding the α-subunit of isoprene monooxygenase, isoA, and DNA stable-isotope probing (DNA-SIP) alone or in combination with other cultivation-independent techniques to determine the abundance, diversity, and activity of isoprene degraders in the environment. These parameters are essential in order to evaluate how microbes might mitigate the effects of this important but neglected climate-active gas. We also suggest key aspects of isoprene metabolism that require further investigation in order to better understand the global isoprene biogeochemical cycle

Exploring Deep-Sea Brines as Potential Terrestrial Analogues of Oceans in the Icy Moons of the Outer Solar System.

Several icy moons of the outer solar system have been receiving considerable attention and are currently seen as major targets for astrobiological research and the search for life beyond our planet. Despite the limited amount of data on the oceans of these moon, we expect them to be composed of brines with variable chemistry, some degree of hydrothermal input, and be under high pressure conditions. The combination of these different conditions significantly limits the number of extreme locations, which can be used as terrestrial analogues. Here we propose the use of deep-sea brines as potential terrestrial analogues to the oceans in the outer solar system. We provide an overview of what is currently known about the conditions on the icy moons of the outer solar system and their oceans as well as on deep-sea brines of the Red Sea and the Mediterranean and their microbiology. We also identify several threads of future research, which would be particularly useful in the context of future exploration of these extra-terrestrial oceans

Diamondoids are not forever: microbial biotransformation of diamondoid carboxylic acids

Oil sands process‐affected waters (OSPW) contain persistent, toxic naphthenic acids (NAs), including the abundant yet little‐studied diamondoid carboxylic acids. Therefore, we investigated the aerobic microbial biotransformation of two of the most abundant, chronically toxic and environmentally relevant diamondoid carboxylic acids: adamantane‐1‐carboxylic acid (A1CA) and 3‐ethyl adamantane carboxylic acid (3EA). We inoculated into minimal salts media with diamondoid carboxylic acids as sole carbon and energy source two samples: (i) a surface water sample (designated TPW) collected from a test pit from the Mildred Lake Settling Basin and (ii) a water sample (designated 2 m) collected at a water depth of 2 m from a tailings pond. By day 33, in TPW enrichments, 71% of A1CA and 50% of 3EA was transformed, with 50% reduction in EC20 toxicity. Similar results were found for 2 m enrichments. Biotransformation of A1CA and 3EA resulted in the production of two metabolites, tentatively identified as 2‐hydroxyadamantane‐1‐carboxylic acid and 3‐ethyladamantane‐2‐ol respectively. Accumulation of both metabolites was less than the loss of the parent compound, indicating that they would have continued to be transformed beyond 33 days and not accumulate as dead‐end metabolites. There were shifts in bacterial community composition during biotransformation, with Pseudomonas species, especially P. stutzeri, dominating enrichments irrespective of the diamondoid carboxylic acid. In conclusion, we demonstrated the microbial biotransformation of two diamondoid carboxylic acids, which has potential application for their removal and detoxification from vast OSPW that are a major environmental threat

Microbial metabolism of isoprene: a much-neglected climate-active gas

The climate-active gas isoprene is the major volatile produced by a variety of trees and is released into the atmosphere in enormous quantities, on a par with global emissions of methane. While isoprene production in plants and its effect on atmospheric chemistry have received considerable attention, research into the biological isoprene sink has been neglected until recently. Here, we review current knowledge on the sources and sinks of isoprene and outline its environmental effects. Focusing on degradation by microbes, many of which are able to use isoprene as the sole source of carbon and energy, we review recent studies characterizing novel isoprene degraders isolated from soils, marine sediments and in association with plants. We describe the development and use of molecular methods to identify, quantify and genetically characterize isoprene-degrading strains in environmental samples. Finally, this review identifies research imperatives for the further study of the environmental impact, ecology, regulation and biochemistry of this interesting group of microbes

Regulation of plasmid-encoded isoprene metabolism in Rhodococcus, a representative of an important link in the global isoprene cycle

Emissions of biogenic volatile organic compounds (VOCs) form an important part of the global carbon cycle, comprising a significant proportion of net ecosystem productivity. They impact atmospheric chemistry and contribute directly and indirectly to greenhouse gases. Isoprene, emitted largely from plants, comprises one third of total VOCs, yet in contrast to methane, which is released in similar quantities, we know little of its biodegradation. Here, we report the genome of an isoprene degrading isolate, Rhodococcus sp. AD45, and, using mutagenesis shows that a plasmid-encoded soluble di-iron centre isoprene monooxygenase (IsoMO) is essential for isoprene metabolism. Using RNA sequencing (RNAseq) to analyse cells exposed to isoprene or epoxyisoprene in a substrate-switch time-course experiment, we show that transcripts from 22 contiguous genes, including those encoding IsoMO, were highly upregulated, becoming among the most abundant in the cell and comprising over 25% of the entire transcriptome. Analysis of gene transcription in the wild type and an IsoMO-disrupted mutant strain showed that epoxyisoprene, or a subsequent product of isoprene metabolism, rather than isoprene itself, was the inducing molecule. We provide a foundation of molecular data for future research on the environmental biological consumption of this important, climate-active compound

Extremely Halophilic Archaeal Communities are Resilient to Short‐Term Entombment in Halite

Some haloarchaea avoid the harsh conditions present in evaporating brines by entombment in brine inclusions within forming halite crystals, where a subset of haloarchaea survives over geological time. However, shifts in the community structure of halite‐entombed archaeal communities remain poorly understood. Therefore, we analysed archaeal communities from in situ hypersaline brines collected from Trapani saltern (Sicily) and their successional changes in brines versus laboratory‐grown halite over 21 weeks, using high‐throughput sequencing. Haloarchaea were dominant, comprising >95% of the archaeal community. Unexpectedly, the OTU richness of the communities after 21 weeks was indistinguishable from the parent brine and overall archaeal abundance in halite showed no clear temporal trends. Furthermore, the duration of entombment was less important than the parent brine from which the halite derived in determining the community composition and relative abundances of most genera in halite‐entombed communities. These results show that halite‐entombed archaeal communities are resilient to entombment durations of up to 21 weeks, and that entombment in halite may be an effective survival strategy for near complete communities of haloarchaea. Additionally, the dominance of ‘halite specialists’ observed in ancient halite must occur over periods of years, rather than months, hinting at long‐term successional dynamics in this environment