Microbial trimethylamine metabolism in marine environments

Trimethylamine (TMA) is common in marine environments. Although the presence of this compound in the oceans has been known for a long time, unlike the mammalian gastrointestinal tract, where TMA metabolism by microorganisms has been studied intensely, many questions remain unanswered about the microbial metabolism of marine TMA. This minireview summarizes what is currently known about the sources and fate of TMA in marine environments and the different pathways and enzymes involved in TMA metabolism in marine bacteria. This review also raises several questions about microbial TMA metabolism in the marine environments and proposes potential directions for future studies.     

Microbial activities in deep subsurface environments

Activities of microorganisms residing in terrestrial deep subsurface sediments were examined in 46 sediment samples from three boreholes. Radiolabeled time course experiments assessing in situ microbial activities were initiated within 30 min of core recovery. [1‐C⁴] Acetate incorporation into lipids, [ methyl‐³H] thymidine incorporation into DNA, [2‐¹⁴C]acetate, and [U‐¹⁴C]glucose mineralization in addition to microbial enrichment and enumeration studies were examined in surface and subsurface sediments. Surface soils contained the greatest biomass and activities, followed by the shallow aquifer zones. Water‐saturated subsurface sands exhibited three to four orders of magnitude greater activity and culturable microorganisms than the dense clay zones, which had low permeability. Regardless of depth, sediments that contained more than 20% clays exhibited the lowest activities and culturable microorganisms.     

Microbial phenotypic heterogeneity and antibiotic tolerance

Phenotypic heterogeneity, defined as metastable variation in cellular parameters generated by epigenetic mechanisms, is crucial for the persistence of bacterial populations under fluctuating selective pressures. Diversity ensures that some individuals will survive a potentially lethal stress, such as an antibiotic, that would otherwise obliterate the entire population. The refractoriness of bacterial infections to antibiotic therapy has been ascribed to antibiotic-tolerant variants known as 'persisters'. The persisters are not drug-resistant mutants and it is unclear why they survive antibiotic pressure that kills their genetically identical siblings. Recent conceptual and technological advances are beginning to yield some surprising new insights into the mechanistic basis of this clinically important manifestation of phenotypic heterogeneity.     

Antibiotics and antibiotic resistance in water environments

Antibiotic-resistant organisms enter into water environments from human and animal sources. These bacteria are able to spread their genes into water-indigenous microbes, which also contain resistance genes. On the contrary, many antibiotics from industrial origin circulate in water environments, potentially altering microbial ecosystems. Risk assessment protocols for antibiotics and resistant bacteria in water, based on better systems for antibiotics detection and antibiotic-resistance microbial source tracking, are starting to be discussed. Methods to reduce resistant bacterial load in wastewaters, and the amount of antimicrobial agents, in most cases originated in hospitals and farms, include optimization of disinfection procedures and management of wastewater and manure. A policy for preventing mixing human-originated and animal-originated bacteria with environmental organisms seems advisable.     

Microbial carbohydrate esterases in cold adapted environments

Psychrophiles produce cold-evolved enzymes that display a high catalytic efficiency, associated with a low thermal stability. In recent years, these enzymes have attracted the attention of scientists because of their peculiar properties that render them particularly useful in investigating the relationship existing between enzyme stability and flexibility on one hand, and enzyme activity on the other hand. Among these enzymes, the esterases, and particularly the feruloyl esterases, have potential uses over a broad range of applications in the agro-food industries. In recent years, the number of microbial feruloyl esterase activities has increased in the growing genome databases. Based on substrate utilization data and supported by primary sequence identity, four subclasses of esterase have been characterized so far. Up to the present, ten genomes from psychrophilic bacteria have been completely sequenced and additional fourteen genomes are under investigation. From the bacteria strains whose genome has been completely sequenced, we analyzed the presence of esterase genes, both the putative genes and the determined experimentally genes, and performed a ClustalW analysis for feruloyl esterases. Major details will be presented for the ORF PSHAa1385 from P. haloplanktis TAC125 that recently has been studied in our research group. In addition, the potential biotechnology applications of this class of enzymes will be discussed.     

Microbial transport: Adaptations to natural environments

The cytoplasmic membrane of bacteria is the matrix for metabolic energy transducing processes such as proton motive force generation and solute transport. Passive permeation of protons across the cytoplasmic membrane is a crucial determinant in the proton motive generating capacity of the organisms. Adaptations of the membrane composition are needed to restrict the proton permeation rates especially at higher temperatures. Thermophilic bacteria cannot sufficiently restrict this proton permeation at their growth temperature and have to rely on the much␣lower permeation of Na + to generate a sodium motive force for driving metabolic energy-dependent membrane processes. Specific transport systems mediate passage across the membrane at physiological rates of all compounds needed for growth and metabolism and of all end products of metabolism. Some of transport systems, the secondary transporters, transduce one form of electrochemical energy into another form. These transporters can play crucial roles in the generation of metabolic energy. This is especially so in anaerobes such as Lactic Acid Bacteria which live under energy-limited conditions. Several transport systems are specifically aimed at the generation of metabolic energy during periods of energy-limitation. In their natural environment bacteria are also often exposed to cytotoxic compounds, including antibiotics. Many bacteria can respond to this live-threatening condition by overexpressing powerful drug-extruding multidrug resistance systems.     

Microbial aspects of atrazine degradation in natural environments

The potential toxicity of thes-triazine herbicide atrazine motivates continuous bioremediation-directed research. Several indigenous soilatrazine-catabolizing microbialassociations and monocultures have been enriched/isolated from compromised sites. Of these, Pseudomonas sp. strain ADP has become a reference strain and has been used to elucidate sequences of the catabolic enzymes atzA, atzB, atzCand atzD involvedin one aerobic degradation pathway and develop probes for the genes which encode these enzymes. Despite this, hitherto unknown or novel microorganisms, with unique sequences and different enzyme-mediated operative pathways, warrant continued investigations for effective site bioremediation. Also, the sustained effectiveness of natural attenuation must be demonstrated continually so regular site evaluations and results analyses, despite the limitations of chemical extraction methodologies, are crucial practices. For both directed and intrinsic bioremediation monitoring, traditional microbial association studies must be complemented by more advanced physiological and molecular approaches. The occurrence of catabolic plasmids, in particular, should be probed with DNA hybridization techniques. Also, PCR-DGGEand subsequent new sequenceelucidation should be used prior to developing new primers for DNA sequences encoding novel catabolic enzymes, and for hybridization probe development, to establish the degradative potential of a compromised site, or adoption of FISH to, for example, monitor bioaugmented remediation.     

Microbial antibiotic production aboard the International Space Station

Previous studies examining metabolic characteristics of bacterial cultures have mostly suggested that reduced gravity is advantageous for microbial growth. As a consequence, the question of whether space flight would similarly enhance secondary metabolite production was raised. Results from three prior space shuttle experiments indicated that antibiotic production was stimulated in space for two different microbial systems, albeit under suboptimal growth conditions. The goal of this latest experiment was to determine whether the enhanced productivity would also occur with better growth conditions and over longer durations of weightlessness. Microbial antibiotic production was examined onboard the International Space Station during the 72-day 8A increment. Findings of increased productivity of actinomycin D by Streptomyces plicatus in space corroborated with previous findings for the early sample points (days 8 and 12); however, the flight production levels were lower than the matched ground control samples for the remainder of the mission. The overall goal of this research program is to elucidate the specific mechanisms responsible for the initial stimulation of productivity in space and translate this knowledge into methods for improving efficiency of commercial production facilities on Earth.     

Microbial dehalogenation of organohalides in marine and estuarine environments

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Microbial responses to microgravity and other low-shear environments.

Microbial adaptation to environmental stimuli is essential for survival. While several of these stimuli have been studied in detail, recent studies have demonstrated an important role for a novel environmental parameter in which microgravity and the low fluid shear dynamics associated with microgravity globally regulate microbial gene expression, physiology, and pathogenesis. In addition to analyzing fundamental questions about microbial responses to spaceflight, these studies have demonstrated important applications for microbial responses to a ground-based, low-shear stress environment similar to that encountered during spaceflight. Moreover, the low-shear growth environment sensed by microbes during microgravity of spaceflight and during ground-based microgravity analogue culture is relevant to those encountered during their natural life cycles on Earth. While no mechanism has been clearly defined to explain how the mechanical force of fluid shear transmits intracellular signals to microbial cells at the molecular level, the fact that cross talk exists between microbial signal transduction systems holds intriguing possibilities that future studies might reveal common mechanotransduction themes between these systems and those used to sense and respond to low-shear stress and changes in gravitation forces. The study of microbial mechanotransduction may identify common conserved mechanisms used by cells to perceive changes in mechanical and/or physical forces, and it has the potential to provide valuable insight for understanding mechanosensing mechanisms in higher organisms. This review summarizes recent and future research trends aimed at understanding the dynamic effects of changes in the mechanical forces that occur in microgravity and other low-shear environments on a wide variety of important microbial parameters.     

Microbial diversity of hypersaline environments: a metagenomic approach

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Microbial diversity in natural environments: focusing on fundamental questions

Interactions with Gijs Kuenen and other Dutch scientists have led my lab to fundamental insights into the composition, structure and function of a hot spring cyanobacterial mat community that should influence our thinking about all microbial communities. By focusing on the distribution of molecular sequence variants of predominant mat phototrophs, we have discovered that small-scale sequence variation can be ecologically meaningful. By applying novel cultivation approaches, we have been able to obtain genetically relevant community members and thus to test the hypothesis that closely related sequence variants arose via adaptive evolutionary radiation. By applying the analytical tools of organic geochemistry we have gained insight into the metabolisms of major phototrophic members of the mat community as well as interactions between phototrophic guilds. These observations challenge traditional paradigms about prokaryotic species and cause us to consider evolutionary ecology theory as we develop genome-based methods for high-resolution analysis of the species-like fundamental units comprising microbial communities, and for investigating how such units coordinate the physiological activities within guilds of the community.     

Inter-species interactions alter antibiotic efficacy in bacterial communities

The efficacy of antibiotic treatments targeting polymicrobial communities is not well predicted by conventional in vitro susceptibility testing based on determining minimum inhibitory concentration (MIC) in monocultures. One reason for this is that inter-species interactions can alter the community members’ susceptibility to antibiotics. Here we quantify, and identify mechanisms for, community-modulated changes of efficacy for clinically relevant antibiotics against the pathogen Pseudomonas aeruginosa in model cystic fibrosis (CF) lung communities derived from clinical samples. We demonstrate that multi-drug resistant Stenotrophomonas maltophilia can provide high levels of antibiotic protection to otherwise sensitive P. aeruginosa. Exposure protection to imipenem was provided by chromosomally encoded metallo-β-lactamase that detoxified the environment; protection was dependent upon S. maltophilia cell density and was provided by S. maltophilia strains isolated from CF sputum, increasing the MIC of P. aeruginosa by up to 16-fold. In contrast, the presence of S. maltophilia provided no protection against meropenem, another routinely used carbapenem. Mathematical ordinary differential equation modelling shows that the level of exposure protection provided against different carbapenems can be explained by differences in antibiotic efficacy and inactivation rate. Together, these findings reveal that exploitation of pre-occurring antimicrobial resistance, and inter-specific competition, can have large impacts on pathogen antibiotic susceptibility, highlighting the importance of microbial ecology for designing successful antibiotic treatments for multispecies communities.Subject terms: Antibiotics, Bacterial infection, Microbial ecology     

Microbial diversity and complexity in hypersaline environments: A preliminary assessment

The microbial communities in solar salterns and a soda lake have been characterized using two techniques: BIOLOG, to estimate the metabolic potential, and amplicon length heterogeneity analysis, to estimate the molecular diversity of these communities. Both techniques demonstrated that the halophilic Bacteria and halophilic Archaea populations in the Eilat, Israel saltern are dynamic communities with extensive metabolic potentials and changing community structures. Halophilic Bacteria were detected in Mono Lake and the lower salinity ponds at the Shark Bay saltern in Western Australia, except when the crystallizer samples were stressed by exposure to Acid Green Dye #9899. At Shark Bay, halophilic Archaea were found only in the crystallizer samples. These data confirm both the metabolic diversity and the phylogenetic complexity of the microbial communities and assert the need to develop more versatile media for the cultivation of the diversity of bacteria in hypersaline environments. Journal of Industrial Microbiology & Biotechnology (2002) 28, 48–55 DOI: 10.1038/sj/jim/7000175 Received 20 May 2001/ Accepted in revised form 15 June 2001     

The prevalence of antibiotic resistance genes among Aeromonas species in aquatic environments

The global rise in antimicrobial resistance (AMR) among bacteria causing infectious diseases is well documented, and the associated risks for human health are well known. There is much less research on AMR with regard to environmental strains, both opportunistic and pathogenic ones. The genus Aeromonas is widely distributed in the environment and causes many variable diseases in fish and humans. Infections in humans are predominantly caused by Aeromonas veronii, A. hydrophila and A. caviae (A. punctata) in a form of bacteremia, gastroenteritis or even septicaemia in immunocompetent and immunocompromised individuals. Different groups of antibiotics are used in the treatment, but studies indicate that fluoroquinolones and cefotaxime are the most efficient. A disturbing consequence of antibiotic overuse is an increasing number of detection of various antibiotic resistance genes (ARG) within this genus. The water environment is one of the major modes of transmission of resistant bacteria from animals to humans, and, thus, the dissemination of antibiotic resistance genes, particularly those located in mobile genetic elements (MGE) occurs in such as plasmids and transposons. This review summarizes recently published information on the type, distribution, and transmission of ARG by MGE, widespread in Aeromonas strains living in various aquatic environments, including wastewater, natural water, aquaculture and urban drinking water. The data available indicate that the opportunistic pathogens like Aeromonas spp. might serve as important vectors of ARG for clinically relevant pathogens present in such bodies of water .