Towards microbial tissue engineering?

Tissue engineering involves the creation of multicellular tissues from individual cells. It was previously perceived that tissues were only formed by higher organisms such as plants and animals. However, it is now known that multicellular systems of microorganisms, such as microbial colonies, biofilms, flocs and aggregates, can also show extensive spatial organization. Here, we discuss methods that can be used to spatially organize microorganisms--bacteria, in particular--into tissue-like materials with defined internal architectures. Some potential uses of such "microbial tissues" are covered.     

Mechanisms of plant and microbial adaptation to heavy metals in plant–microbial systems

The data on heavy metal (HM) accumulation and detoxification by plants and bacteria in plant–microbial systems (PMS) are reviewed. Bacteria are shown to be the labile component of the system, responsible for a considerable amelioration of HM stress impact on plants and for improved PMS adaptation to heavy metals. Simulation of plant–microbial interactions under conditions of soil contamination by HM revealed the protective role of bacterial migration from the rhizoplane to the rhizosphere.     

Influence of microbial activity on plant–microbial competition for organic and inorganic nitrogen

To investigate how the level of microbial activity in grassland soils affects plant–microbial competition for different nitrogen (N) forms, we established microcosms consisting of a natural soil community and a seedling of one of two co-existing grass species, Anthoxanthum odoratum or Festuca rubra. We then stimulated the soil microbial community with glucose in half of the microcosms and followed the transfer of added inorganic (¹⁵NH₄¹⁵NO₃) and organic (glycine-2-¹³C-¹⁵N) N into microbial and plant biomass. We found that microbes captured significantly more ¹⁵N in organic than in inorganic form and that glucose addition increased microbial ¹⁵N capture from the inorganic source. Shoot and root biomass, total shoot N content and shoot and root ¹⁵N contents were significantly greater for A. odoratum than F. rubra, whereas F. rubra had higher shoot and root N concentrations. Where glucose was not added, A. odoratum had higher shoot ¹⁵N content with organic than with inorganic ¹⁵N addition, whereas where glucose was added, both species had higher shoot ¹⁵N content with inorganic than with organic ¹⁵N. Glucose addition had equally negative effects on shoot growth, total shoot N content, shoot and root N concentrations and shoot and root ¹⁵N content for both species. Both N forms produced significantly more shoot biomass and higher shoot N content than the water control, but the chemical form of N had no significant effect. Our findings suggest that plant species that are better in capturing nutrients from soil are not necessarily better in tolerating increasing microbial competition for nutrients. It also appears that intense microbial competition has more adverse effects on the uptake of organic than inorganic N by plants, which may potentially have significant implications for interspecific plant–plant competition for N in ecosystems where the importance of organic N is high and some of the plant species specialize in use of organic N.     

Plant–microbial competition for nitrogen increases microbial activities and carbon loss in invaded soils

Many invasive plant species show high rates of nutrient acquisition relative to their competitors. Yet the mechanisms underlying this phenomenon, and its implications for ecosystem functioning, are poorly understood, particularly in nutrient-limited systems. Here, we test the hypothesis that an invasive plant species (Microstegium vimineum) enhances its rate of nitrogen (N) acquisition by outcompeting soil organic matter-degrading microbes for N, which in turn accelerates soil N and carbon (C) cycling. We estimated plant cover as an indicator of plant N acquisition rate and quantified plant tissue N, soil C and N content and transformations, and extracellular enzyme activities in invaded and uninvaded plots. Under low ambient N availability, invaded plots had 77% higher plant cover and lower tissue C:N ratios, suggesting that invasion increased rates of plant N acquisition. Concurrent with this pattern, we observed significantly higher mass-specific enzyme activities in invaded plots as well as 71% higher long-term N availability, 21% lower short-term N availability, and 16% lower particulate organic matter N. A structural equation model showed that these changes were interrelated and associated with 27% lower particulate organic matter C in invaded areas. Our findings suggest that acquisition of N by this plant species enhances microbial N demand, leading to an increased flux of N from organic to inorganic forms and a loss of soil C. We conclude that high N acquisition rates by invasive plants can drive changes in soil N cycling that are linked to effects on soil C.     

Hydrogen sulfide: clandestine microbial messenger?

Although the toxicity of hydrogen sulfide (H(2)S) has been substantiated for almost 230 years, its pivotal roles in both aerobic and anaerobic organisms have only recently become evident. In low oxygen environments with millimolar concentrations of H(2)S, it functions as an electron donor and as an energy source in some systems. At micromolar levels, intracellular H(2)S in aerobic organisms has a vital role in redox balancing. At even lower concentrations, H(2)S provides essential signals in yeast, in the brain and in smooth and cardiac muscles. Here, other possible coordinating roles within and between microorganisms are suggested, including the possibility that H(2)S functions as a signalling mediator in prokaryotes. It is expected that future research will uncover a host of novel functions, not only in eukaryotes but also in prokaryotic species.     

What can microbial genetics teach sociobiology?

Progress in our understanding of sociobiology has occurred with little knowledge of the genetic mechanisms that underlie social traits. However, several recent studies have described microbial genes that affect social traits, thereby bringing genetics to sociobiology. A key finding is that simple genetic changes can have marked social consequences, and mutations that affect cheating and recognition behaviors have been discovered. The study of these mutants confirms a central theoretical prediction of social evolution: that genetic relatedness promotes cooperation. Microbial genetics also provides an important new perspective: that the genome-to-phenome mapping of social organisms might be organized to constrain the evolution of social cheaters. This constraint can occur both through pleiotropic genes that link cheating to a personal cost and through the existence of phoenix genes, which rescue cooperative systems from selfish and destructive strategies. These new insights show the power of studying microorganisms to improve our understanding of the evolution of cooperation.     

Did surface temperatures constrain microbial evolution?

The proposition that glaciation may not have occurred before the Cenozoic--albeit not yet a consensus position--nevertheless raises for reconsideration the surface temperature history of the earth. Glacial episodes, from the Huronian (2.3 billion years ago; BYA) through the late Paleozoic (320 to 250 million years ago; MYA) have been critical constraints on estimation of the upper bounds of temperature (Crowley 1983, Kasting and Toon 1989). Once removed, few if any constraints on the upper temperature limit other than life remain. Walker (1982) recognized that life provides an upper limit to temperature in the Precambrian. We propose a more radical concept: the upper temperature limit for viable growth of a given microbial group corresponds to the actual surface temperature at the time of the group's first appearance. In particular, we propose here that two major evolutionary developments--the emergence of cyanobacteria and aerobic eukaryotes--can be used to determine surface temperature in the Precambrian, and that only subsequent cooling mediated by higher plants and then angiosperms permitted what may possibly be the earth's first glaciation in the late Cenozoic.     

Can transgenic maize affect soil microbial communities?

The aim of the experiment was to determine if temporal variations of belowground activity reflect the influence of the Cry1Ab protein from transgenic maize on soil bacteria and, hence, on a regulatory change of the microbial community (ability to metabolize sources belonging to different chemical guilds) and/or a change in numerical abundance of their cells. Litter placement is known for its strong influence on the soil decomposer communities. The effects of the addition of crop residues on respiration and catabolic activities of the bacterial community were examined in microcosm experiments. Four cultivars of Zea mays L. of two different isolines (each one including the conventional crop and its Bacillus thuringiensis cultivar) and one control of bulk soil were included in the experimental design. The growth models suggest a dichotomy between soils amended with either conventional or transgenic maize residues. The Cry1Ab protein appeared to influence the composition of the microbial community. The highly enhanced soil respiration observed during the first 72 h after the addition of Bt-maize residues can be interpreted as being related to the presence of the transgenic crop residues. This result was confirmed by agar plate counting, as the averages of the colony-forming units of soils in conventional treatments were about one-third of those treated with transgenic straw. Furthermore, the addition of Bt-maize appeared to induce increased microbial consumption of carbohydrates in BIOLOG EcoPlates. Three weeks after the addition of maize residues to the soils, no differences between the consumption rate of specific chemical guilds by bacteria in soils amended with transgenic maize and bacteria in soils amended with conventional maize were detectable. Reaped crop residues, comparable to post-harvest maize straw (a common practice in current agriculture), rapidly influence the soil bacterial cells at a functional level. Overall, these data support the existence of short Bt-induced ecological shifts in the microbial communities of croplands' soils.     

Hydrogeologic parameters affecting vadose‐zone microbial distributions

Abstract

The vadose zone and its contaminant‐attenuating processes are physically interposed between surface contamination and groundwater supplies. Given the potential role of microorganisms in mediating vadose‐zone chemical processes, it is vital to understand vadose microbial distributions and factors controlling those distributions. Vadose and shallow saturated zone sediments obtained from cores drilled to approximately 8 m below the surface at two hydrogeologically contrasting sites, named Dalmeny and Washington State University (WSU), were examined for culturable heterotrophic bacteria, total organic carbon (TOC), and sediment texture. Pore‐water elutions were analyzed for dissolved organic carbon, sulfate, and inorganic nitrogen species. Numbers of cultured bacteria (10³‐10⁷ g^?1) generally decreased with depth at both sites. The TOC decreased uniformly with depth at WSU where soil processes are the sole carbon source; at Dalmeny, where both soil and kerogen carbon are present, TOC was higher and relatively constant with depth. Numbers of distinct colony types at Dalmeny did not decline below the solum. Bacteria at Dalmeny were more numerous, exhibited greater numbers of colony types, and were metabolically more flexible than those at WSU. The smooth decline of numbers with depth at WSU paralleled and may be caused by the TOC decline with distance from a solum source. Sediment permeability and pore‐water flux did not control bulk populations as suggested in previous studies; this may be explained by bacterial residence on fracture surfaces in low‐permeability materials. Psychrotolerant organisms did not appear to be as abundant as mean ambient temperatures might suggest.     

Triggers for microbial aggregation in activated sludge?

 Microbial aggregation into good settling sludge is essential for the well-functioning of activated sludge systems treating waste water. Complete aggregation of all the microbial biomass formed has been proven to be difficult to maintain continuously, resulting in wash-out of suspended solids. This review investigates the possibility that environmental signals could constitute triggers for the induction or stimulation of aggregative physiology. Received: 24 August 1995/Accepted: 7 September 1995     

Winter microbial activity in Lake Tuusulanjärvi

Microbial heterotrophic activity, dark CO₂ assimilation, primary productivity and microbial ATP were measured monthly in the extremely eutrophic Lake Tuusulanjärvi during the winter of 1979–1980. Because of continuous water circulation caused by low temperature and artificial aeration of the lake, no winter stratification developed. Very low summertime ³H-glucose turnover times of 5 h increased to a level of 10–20 h from August to January. Winter maximum of 110 h was measured in March, and turnover times returned to 10–20 h in April, before the vernal bloom of algae occured. Oxygen saturation remained over 46% during the winter.High primary productivity was observed in November (400–500 mg C m^–3 day^–1), and measurable productivity was detected under ice in January (80 mg C m^–3 day^–1). Dark CO₂ assimilation increased to 14% of primary productivity in March. No correlation was found between ³H-glucose turnover rate and dark CO₂ assimilation. ATP correlated slightly better with primary productivity than with turnover rate. The single concentration method proved to be sensitive for winter heterotrophic activity measurement.     

Are viruses driving microbial diversification and diversity?

Viruses can influence the genetic diversity of prokaryotes in various ways. They can affect the community composition of prokaryotes by 'killing the winner' and keeping in check competitive dominants. This may sustain species richness and the amount of information encoded in genomes. Viruses can also transfer (viral and host) genes between species. Such mechanisms have probably influenced the speciation of prokaryotes. Whole-genome sequencing has clearly revealed the importance of (virus-mediated) gene transfer. However, its significance for the ecological performance of aquatic microbial communities is only poorly studied, although the few available reports indicate a large potential. Here, we present data supporting the hypothesis that viral genes and viral activity generate genetic variability of prokaryotes and are a driving force for ecological functioning and evolutionary change.     

Bioinformatics in microbial biotechnology – a mini review

The revolutionary growth in the computation speed and memory storage capability has fueled a new era in the analysis of biological data. Hundreds of microbial genomes and many eukaryotic genomes including a cleaner draft of human genome have been sequenced raising the expectation of better control of microorganisms. The goals are as lofty as the development of rational drugs and antimicrobial agents, development of new enhanced bacterial strains for bioremediation and pollution control, development of better and easy to administer vaccines, the development of protein biomarkers for various bacterial diseases, and better understanding of host-bacteria interaction to prevent bacterial infections. In the last decade the development of many new bioinformatics techniques and integrated databases has facilitated the realization of these goals. Current research in bioinformatics can be classified into: (i) genomics – sequencing and comparative study of genomes to identify gene and genome functionality, (ii) proteomics – identification and characterization of protein related properties and reconstruction of metabolic and regulatory pathways, (iii) cell visualization and simulation to study and model cell behavior, and (iv) application to the development of drugs and anti-microbial agents. In this article, we will focus on the techniques and their limitations in genomics and proteomics. Bioinformatics research can be classified under three major approaches: (1) analysis based upon the available experimental wet-lab data, (2) the use of mathematical modeling to derive new information, and (3) an integrated approach that integrates search techniques with mathematical modeling. The major impact of bioinformatics research has been to automate the genome sequencing, automated development of integrated genomics and proteomics databases, automated genome comparisons to identify the genome function, automated derivation of metabolic pathways, gene expression analysis to derive regulatory pathways, the development of statistical techniques, clustering techniques and data mining techniques to derive protein-protein and protein-DNA interactions, and modeling of 3D structure of proteins and 3D docking between proteins and biochemicals for rational drug design, difference analysis between pathogenic and non-pathogenic strains to identify candidate genes for vaccines and anti-microbial agents, and the whole genome comparison to understand the microbial evolution. The development of bioinformatics techniques has enhanced the pace of biological discovery by automated analysis of large number of microbial genomes. We are on the verge of using all this knowledge to understand cellular mechanisms at the systemic level. The developed bioinformatics techniques have potential to facilitate (i) the discovery of causes of diseases, (ii) vaccine and rational drug design, and (iii) improved cost effective agents for bioremediation by pruning out the dead ends. Despite the fast paced global effort, the current analysis is limited by the lack of available gene-functionality from the wet-lab data, the lack of computer algorithms to explore vast amount of data with unknown functionality, limited availability of protein-protein and protein-DNA interactions, and the lack of knowledge of temporal and transient behavior of genes and pathways.     

Is the microbial tree of life verificationist?

The field of microbial phylogenetics has questioned the feasibility of using a tree‐like structure to the describe microbial evolution. This debate centres on two main points. First, because microorganisms are able to transfer genes from one to another in zero generations (horizontal gene transfer, or HGT), the use of molecular characters to perform phylogenetic analyses will yield an erroneous topology and HGT clearly makes the evolution of microorganisms non tree‐like. Second, the use of concatenated gene sequences in a total evidence approach to phylogenetic systematics is a verificationist endeavour, the aim of which is to bolster support. However, the goal of the total evidence approach to phylogenetic research is based in the idea of increasing explanatory power over background knowledge through test and corroboration, rather than to bolster support for nodes in a tree. In this context, the testing of phylogenetic data is a falsificationist endeavour that includes the possibility of not rejecting the null hypothesis that there is no tree‐like structure in molecular phylogenetic data. We discuss several tests that aim to test rigorously the hypothesis that a tree of life exists for microorganisms. We also discuss the philosophical ramifications of background knowledge and corroboration in microbial studies that need to be considered when suggesting that HGT confounds the tree of life. © The Willi Hennig Society 2009.     

Does plant community plasticity mediate microbial homeostasis?

Microbial homeostasis—constant microbial element ratios along resource gradients—is a core ecological tenet, yet not all systems display homeostasis. We suggest investigations of homeostasis mechanisms must also consider plant–microbial interactions. Specifically, we hypothesized that ecosystems with strong plant community plasticity to changing resources will have homeostatic microbial communities, with less microbial resource cost, because plants reduce variance in resource stoichiometry. Using long‐term nutrient additions in two ecosystems with differing plant response, we fail to support our hypothesis because although homeostasis appears stronger in the system with stronger plant response, microbial mechanisms were also stronger. However, our conclusions were undermined by high heterogeneity in resources, which may be common in ecosystem‐level studies, and methodological assumptions may be exacerbated by shifting plant communities. We propose our study as a starting point for further ecosystem‐scale investigations, with higher replication to address microbial and soil variability, and improved insight into microbial assimilable resources.     

Forest fire may disrupt plant–microbial feedbacks

Plant–microbial feedbacks are important drivers of plant community structure and dynamics. These feedbacks are driven by the variable modification of soil microbial communities by different plant species. However, other factors besides plant species can influence soil communities and potentially interact with plant–microbial feedbacks. We tested for plant–microbial feedbacks in two Eucalyptus species, E. globulus and E. obliqua, and the influence of forest fire on these feedbacks. We collected soils from beneath mature trees of both species within native forest stands on the Forestier Peninsula, Tasmania, Australia, that had or had not been burnt by a recent forest fire. These soils were subsequently used to inoculate seedlings of both species in a glasshouse experiment. We hypothesized that (i) eucalypt seedlings would respond differently to inoculation with conspecific versus heterospecific soils (i.e., exhibit plant–microbial feedbacks) and (ii) these feedbacks would be removed by forest fire. For each species, linear mixed effects models tested for differences in seedling survival and biomass in response to inoculation with conspecific versus heterospecific soils that had been collected from either unburnt or burnt stands. Eucalyptus globulus displayed a response consistent with a positive plant–microbial feedback, where seedlings performed better when inoculated with conspecific versus heterospecific soils. However, this effect was only present when seedlings were inoculated with unburnt soils, suggesting that fire removed the positive effect of E. globulus inoculum. These findings show that external environmental factors can interact with plant–microbial feedbacks, with possible implications for plant community structure and dynamics.     

What role does pyroptosis play in microbial infection?

Pyroptosis, a type of programmed cell death mediated by gasdermin, is characterized by the swelling and rupture of cells, release of cellular contents and a strong inflammatory response, which is critical for controlling microbial infection. Pattern recognition receptors recognize the intracellular and extracellular pathogenic microbial components and stimulate the organism's inflammatory response by activating the pyroptosis signaling pathway and releasing interleukin-1β (IL-1β), IL-18, and other inflammatory factors to promote pathogen clearance and prevent infection. In the process of continuous evolution, pathogens have developed multiple strategies to modulate the occurrence of pyroptosis and thus enhance their ability to induce disease; that is, the competition between host cells and pathogens controls the occurrence of pyroptosis. Competition can directly affect tissue inflammation outbreaks and even alter cell survival. Studies have shown that various bacterial infections, including Shigella flexneri, Salmonella, Listeria monocytogenes, and Legionella pneumophila, can lead to pyroptosis. Pyroptosis is associated with the occurrence and development of various diseases caused by microbial infection, and the identification of molecules related to the pyroptosis signaling pathway may provide new drug targets for the treatment of related diseases. This study reviews the molecular mechanisms of pyroptosis and the role of pyroptosis in microbial infection-related diseases.