Trait-based life-history strategies explain succession scenario for complex bacterial communities under varying disturbance

Trait-based approaches are increasingly gaining importance in community ecology, as a way of finding general rules for the mechanisms driving changes in community structure and function under the influence of perturbations. Frameworks for life-history strategies have been successfully applied to describe changes in plant and animal communities upon disturbance. To evaluate their applicability to complex bacterial communities, we operated replicated wastewater treatment bioreactors for 35 days and subjected them to eight different disturbance frequencies of a toxic pollutant (3-chloroaniline), starting with a mixed inoculum from a full-scale treatment plant. Relevant ecosystem functions were tracked and microbial communities assessed through metagenomics and 16S rRNA gene sequencing. Combining a series of ordination, statistical and network analysis methods, we associated different life-history strategies with microbial communities across the disturbance range. These strategies were evaluated using tradeoffs in community function and genotypic potential, and changes in bacterial genus composition. We further compared our findings with other ecological studies and adopted a semi-quantitative competitors, stress-tolerants, ruderals (CSR) classification. The framework reduces complex data sets of microbial traits, functions and taxa into ecologically meaningful components to help understand the system response to disturbance and hence represents a promising tool for managing microbial communities.     

General approach to bacterial nutrition: growth factor requirements of Moraxella nonliquefaciens.

A general procedure was devised for the determination of growth factor requirements of heterotrophic bacteria based upon identification of individual nutrients as they are successively depleted from a limited quantity of complex medium. By using this approach, it was possible to develop a defined medium for growth of Moraxella nonliquefaciens that contained nine amino acids and three vitamins. Three of the amino acids, proline, serine, and cysteine, were required in unusually high concentrations to obtain optimal growth. Methionine had a sparing action on the requirements for serine and cysteine. Glycine could substitute for serine. Although a required nutrient, cysteine was inhibitory for growth, but this inhibitory action was antagonized by valine or leucine. The requirement for cysteine was satisfied by cystine, glutathione, or sodium sulfide. M. nonliquefaciens could not use ammonia as a nitrogen source but could use glutamate or aspartate for this purpose. With the exception of 1 auxotrophic strain, the growth factor requirements of 23 independently isolated strains of M. nonliquefaciens were essentially the same.     

Trait-based approaches reveal fungal adaptations to nutrient-limiting conditions

The dependency of microbial activity on nutrient availability in soil is only partly understood, but highly relevant for nutrient cycling dynamics. In order to achieve more insight on microbial adaptations to nutrient limiting conditions, precise physiological knowledge is needed. Therefore, we developed an experimental system assessing traits of 16 saprobic fungal isolates in nitrogen (N) limited conditions. We tested the hypotheses that (1) fungal traits are negatively affected by N deficiency to a similar extent and (2) fungal isolates respond in a phylogenetically conserved fashion. Indeed, mycelial density, spore production and fungal activity (respiration and enzymatic activity) responded similarly to limiting conditions by an overall linear decrease. By contrast, mycelial extension and hyphal elongation peaked at lowest N supply (C:N 200), causing maximal biomass production at intermediate N contents. Optimal N supply rates differed among isolates, but only the extent of growth reduction was phylogenetically conserved. In conclusion, growth responses appeared as a switch from explorative growth in low nutrient conditions to exploitative growth in nutrient-rich patches, as also supported by responses to phosphorus and carbon limitations. This detailed trait-based pattern will not only improve fungal growth models, but also may facilitate interpretations of microbial responses observed in field studies.     

Trait-based species richness: ecology and macroevolution

Understanding the origins of species richness patterns is a fundamental goal in ecology and evolutionary biology. Much research has focused on explaining two kinds of species richness patterns: (i) spatial species richness patterns (e.g. the latitudinal diversity gradient), and (ii) clade-based species richness patterns (e.g. the predominance of angiosperm species among plants). Here, I highlight a third kind of richness pattern: trait-based species richness (e.g. the number of species with each state of a character, such as diet or body size). Trait-based richness patterns are relevant to many topics in ecology and evolution, from ecosystem function to adaptive radiation to the paradox of sex. Although many studies have described particular trait-based richness patterns, the origins of these patterns remain far less understood, and trait-based richness has not been emphasised as a general category of richness patterns. Here, I describe a conceptual framework for how trait-based richness patterns arise compared to other richness patterns. A systematic review suggests that trait-based richness patterns are most often explained by when each state originates within a group (i.e. older states generally have higher richness), and not by differences in transition rates among states or faster diversification of species with certain states. This latter result contrasts with the widespread emphasis on diversification rates in species-richness research. I show that many recent studies of spatial richness patterns are actually studies of trait-based richness patterns, potentially confounding the causes of these patterns. Finally, I describe a plethora of unanswered questions related to trait-based richness patterns.     

Heterotrophic bacterial growth efficiency and community structure at different natural organic carbon concentrations

Batch cultures of aquatic bacteria and dissolved organic matter were used to examine the impact of carbon source concentration on bacterial growth, biomass, growth efficiency, and community composition. An aged concentrate of dissolved organic matter from a humic lake was diluted with organic compound-free artificial lake water to obtain concentrations of dissolved organic carbon (DOC) ranging from 0.04 to 2.53 mM. The bacterial biomass produced in the cultures increased linearly with the DOC concentration, indicating that bacterial biomass production was limited by the supply of carbon. The bacterial growth rate in the exponential growth phase exhibited a hyperbolic response to the DOC concentration, suggesting that the maximum growth rate was constrained by the substrate concentration at low DOC concentrations. Likewise, the bacterial growth efficiency calculated from the production of biomass and CO(2) increased asymptotically from 0.4 to 10.4% with increasing DOC concentration. The compositions of the microbial communities that emerged in the cultures were assessed by separation of PCR-amplified 16S rRNA fragments by denaturing gradient gel electrophoresis. Nonmetric multidimensional scaling of the gel profiles showed that there was a gradual change in the community composition along the DOC gradient; members of the beta subclass of the class Proteobacteria and members of the Cytophaga-Flavobacterium group were well represented at all concentrations, whereas members of the alpha subclass of the Proteobacteria were found exclusively at the lowest carbon concentration. The shift in community composition along the DOC gradient was similar to the patterns of growth efficiency and growth rate. The results suggest that the bacterial growth efficiencies, the rates of bacterial growth, and the compositions of bacterial communities are not constrained by substrate concentrations in most natural waters, with the possible exception of the most oligotrophic environments.     

Thermodynamic efficiency of bacterial growth calculated from growth yield of Pseudomonas oxalaticus OX1 in the chemostat

In order to determine the thermodynamic efficiency of bacterial growth, Pseudomonas oxalaticus OX1 was grown in carbon-limited continuous cultures. 11 different carbon sources, ranging from oxalate (most oxidised component) to ethanol (most reduced component), were used as limiting substrate in these experiments. From the experimental yield values (expressed as C-mol dry weight produced per C-mol carbon substrate consumed) the thermodynamic efficiencies were calculated. On substrates more reduced than biomass (such as ethanol and glycerol) the thermodynamic efficiency of growth of P. oxalaticus was negative but it reached a maximum of 23 +/- 3% with substrates with a degree of reduction of 3 (citrate) and lower. The actual concentrations of the components involved were incorporated into the calculations but this affected the overall thermodynamic efficiency only to a small extent. This result strengthens the conclusion of Westerhoff et al. (Westerhoff, H.V., Hellingwerf, K.J. and Van Dam, K. (1983) Proc. Natl. Acad. Sci. 80, 305-309) that bacteria have been optimised towards a theoretical thermodynamic efficiency of 24%, corresponding with maximisation of growth rate at optimal efficiency, with highly oxidised substrates.     

Trait-based approaches to predicting biological control success: challenges and prospects

Identifying traits that are associated with success of introduced natural enemies in establishing and controlling pest insects has occupied researchers and biological control practitioners for decades. Unfortunately, consistent general relationships have been difficult to detect, preventing a priori ranking of candidate biological control agents based on their traits. We summarise previous efforts and propose a series of potential explanations for the lack of clear patterns. We argue that the quality of current datasets is insufficient to detect complex trait–efficacy relationships and suggest several measures by which current limitations may be overcome. We conclude that efforts to address this elusive issue have not yet been exhausted and that further explorations are likely to be worthwhile.     

Low bacterial growth efficiency in the oligotrophic eastern Mediterranean Sea: a modelling analysis

Bacterial growth efficiency (BGE) is generally related to thetrophic status of marine systems, with values as low as 0.15or less associated with the most nutrient-depleted areas. Asimple steady-state model is used to examine whether the observedratio of bacterial to primary production (BP:PP) of 0.22 inthe eastern Mediterranean Sea, an ultra-oligotrophic system,can be sustained given a BGE of 0.15. There is no a priori reasonto believe that BGE should be higher in this area relative toother open ocean environments, although accurate measurementsare required to investigate this possibility. The model includesprimary production [both particulate and exudation of dissolvedmaterial expressed as a percentage of extracellular release(PER)] and terriginous dissolved organic carbon (DOC) as sources,cycling via zooplankton, viruses and bacteria, and bacterialand zooplanktonrespiration as sinks for carbon. Results indicatethat a BP:PP of 0.22 cannot be maintained if bacterial carbondemand is met solely with DOC of autochthonous origin, givena BGE of 0.15. Sufficient carbon is, however, supplied to maintainthis ratio if a high phytoplankton exudation of DOC (PER = 40%)is permitted, in conjunction with a BGE of 0.16. A BGE of 0.28is required if PER takes on a more typical value of 10%. Thepossibility of BP being significantly enhanced by DOC of terrestrialorigin is discounted, there being no major riverine sourcesnear the Cretan Sea. Our analysis emphasizes the need for accurateestimates of BGE, and an improved understanding of sources andsinks of organic carbon, in marine systems.     

Sea ice bacterial growth rate, growth efficiency and preference for inorganic nitrogen sources in the Baltic Sea

Seasonal Baltic Sea ice is structurally similar to polar sea ice and provides habitats for diverse ice organism assemblages that are integral to the biogeochemistry and ecology of the sea during winter. Temperature and inorganic nitrogen sources have been suggested to control bacterial growth, with increasing dependence on ammonium at low temperatures. To study the bacterial growth and preference for the nitrogen source, we conducted experiments at 0 and 4°C, using ammonium and nitrate as nitrogen sources at two coastal fast-ice stations in the Gulf of Finland and in the Gulf of Bothnia during three successive winters. The two study sites differ markedly in relation to the allochthonous dissolved organic matter supply from the catchment area. High levels of bacterial growth were recorded at both study sites, with community generation times of 15–37 h. The measured bacterial growth efficiencies of 20–58% suggest that the Baltic sea ice brines provide a rich medium for bacterial growth and efficient functioning of bacteria-based food webs. Our experiments with sea ice samples showed a preference for ammonium at both temperatures and high potential growth in both types of nitrogen supplies. No major differences in phosphorus depletion rates were found at the two temperatures, but rates were always highest when ammonium was added to the experiments. These experiments point out that ice maturity, presumably through changes in bacterial community structure, impacts nitrogen processes and that these processes are pronounced prior to melting of the ice.     

Simulated bacterial growth

A mathematical model system for the simulation of bacterial growth is presented, based on eight observable growth parameters used as input. These parameters reflect the chain elongation rates of DNA, RNA and protein, the control of stable RNA and RNA polymerase genes, the functional activities of ribosomes and RNA polymerase, and the control of DNA replication and cell division. With observed values for these parameters, the model system simulates the exponential increase in the number of ribosomes and RNA polymerase molecules, as well as in the amounts of DNA, RNA and protein and in the cell number. The doubling time of this exponential increase and the simulated cell composition (DNA, RNA and protein per cell, or RNA and protein per genome) assume the correct values typical for the culture in which the input parameters were observed, and independent of the zero time conditions of the system which can be arbitrarily chosen. The simulation can be used to check the consistency of observed growth parameters, or to indirectly find the kinetic behavior of growth parameters which cannot be readily observed, or to analyze experiments involving a perturbation of steady-state growth. As examples of the latter, the simulation of a “step-up” experiment is presented in which the effects of a step-wise increase in the DNA replication velocity are analyzed, and the simulation of a nutritional shift-up, in which the kinetic changes in the gene activities for rRNA and rprotein genes are examined.     

Recurrent seasonal changes in bacterial growth efficiency,metabolism and community composition in coastal waters

The microbial response to environmental changes in coastal waters of the eastern Cantabrian Sea was explored for four years by analysing a broad set of environmental variables along with bacterial community metabolism and composition. A recurrent seasonal cycle emerged, consisting of two stable periods, characterized by low bacterial metabolic activity (winter) from October to March, and high bacterial metabolic activity (summer) from May to August. These two contrasting periods were linked by short transition periods in April (T_A) and September (T_S). The phylogenetic groups Alphaproteobacteria and Bacteroidetes were dominant during winter and summer respectively, and their recurrent alternation was mainly driven by the bloom of eukaryotic phytoplankton before T_A and the bloom of prokaryotic phytoplankton before T_S. Bacterial growth efficiency remained high and stable during the winter and summer periods but dropped during the two short transition periods. Our results suggest that bacterial growth efficiency should be considered a very resilient property that reflects different stages in the adaptation of the bacterial community composition to the environmental changes occurring throughout the seasonal cycle in this coastal ecosystem.     

A new mathematical approach predicts individual cell growth behavior using bacterial population information

A theoretical methodology has been developed for studying the growth kinetics of bacterial cells. It utilizes the steady-state cell length distribution in a bacterial population to predict the dependency of growth and division rates on cell length and age. The mathematical model has been applied to the analysis of two bacterial populations, a wild-type strain of Bacillus subtilis, and a minicell-producing strain that carries the divIVB1 mutation. The results show that our model describes the wild-type population very well and that the assumptions typically used in traditional methods are unrealistic. In the case of the minicell-producing mutant we find evidence that the rate of cell division must be a function not only of cell size but also of cell age.     

Phage reproduction in relation to bacterial growth rate

Summary The reproduction of bacteriophages T₁–T₇ inE. coli B growing in a continuous culture apparatus at constant generation times of 50′ and 150′ was studied in a defined medium with a high concentration of glucose and in a medium with glucose as a limiting factor. It was shown that the propagation rate (as measured by the latent period) of phages T₂, T₄, T₆ and T₇ decreased with longer bacterial generation times and with reduced energy- and carbon-supply. In contrast the reproduction of phages T₁, T₃ and T₅ (which are mainly synthesized from the contents of the host cell) was unaffected by the slowing down of bacterial metabolism.     

Investigation of an expert systems approach to bacterial identification

An investigation was carried out to assess the feasibility ofusing an expert systems approach to assist in the identificationof unknown isolates of bacteria. A system was developed usingLisp which utilized the knowledge stored in standard bacteriologicaltexts. A comparison of the expert systems approach and the probabilisticapproach based on Bayes Theorem was made together with the advantagesand disadvantages of each approach. Received on November 5, 1990; accepted on February 20, 1991     

Single-molecule approach to bacterial genomic comparisons via optical mapping

Modern comparative genomics has been established, in part, by the sequencing and annotation of a broad range of microbial species. To gain further insights, new sequencing efforts are now dealing with the variety of strains or isolates that gives a species definition and range; however, this number vastly outstrips our ability to sequence them. Given the availability of a large number of microbial species, new whole genome approaches must be developed to fully leverage this information at the level of strain diversity that maximize discovery. Here, we describe how optical mapping, a single-molecule system, was used to identify and annotate chromosomal alterations between bacterial strains represented by several species. Since whole-genome optical maps are ordered restriction maps, sequenced strains of Shigella flexneri serotype 2a (2457T and 301), Yersinia pestis (CO 92 and KIM), and Escherichia coli were aligned as maps to identify regions of homology and to further characterize them as possible insertions, deletions, inversions, or translocations. Importantly, an unsequenced Shigella flexneri strain (serotype Y strain AMC[328Y]) was optically mapped and aligned with two sequenced ones to reveal one novel locus implicated in serotype conversion and several other loci containing insertion sequence elements or phage-related gene insertions. Our results suggest that genomic rearrangements and chromosomal breakpoints are readily identified and annotated against a prototypic sequenced strain by using the tools of optical mapping.     

A rule-based approach to the modelling of bacterial ecosystems

This paper presents an approach to ecological/evolutionary modelling that is inspired by natural bacterial ecosystems and bacterial evolution. An individual-based artificial ecosystem model is proposed, which is designed to explore the evolvability of adaptive behavioural strategies in artificial bacteria represented by rule-based learning classifier systems. The proposed ecosystem model consists of a n-dimensional environmental grid, which can contain different types of artificial resources in arbitrary arrangements. The resources provide the energy that is necessary for the organisms to sustain life, and can trigger different types of behaviour in the organisms, such as movement towards nutrients and away from toxic substances, growth, and the controlled release of signalling resources. The balance between energy and material is modelled carefully to ensure that the ecosystem is dissipative. Those organisms that are able to efficiently exploit the available resources gradually accumulate enough energy to reproduce (by binary fission) and generate copies of themselves in the environment. Organisms are also able to produce their own resources, which can potentially be used as markers to send signals to other organisms (a behaviour known as quorum sensing). The complex relationships between stimuli and actions in the organisms are stochastically altered by means of mutations, thus enabling the organisms to adapt to their environment and maximise their lifespan and reproductive success. In this paper, the proposed bacterial ecosystem model is defined formally and its structure is discussed in detail. This is followed by results from simulation experiments that illustrate the model's operation and how it can be used in evolutionary modelling/computing scenarios.     

Comparative approach to capture bacterial diversity of coastal waters

Despite the revolutionary advancements in DNA sequencing technology and cultivation techniques, few studies have been done to directly compare these methods. In this study, a 16S rRNA gene-based, integrative approach combining culture-independent techniques with culture-dependent methods was taken to investigate the bacterial community structure of coastal seawater collected from the Yellow Sea, Korea. For culture-independent studies, we used the latest model pyrosequencer, Roche/454 Genome Sequencer FLX Titanium. Pyrosequencing captured a total of 52 phyla including 27 candidate divisions from the water column, whereas the traditional cloning approach captured only 15 phyla including 2 candidate divisions. In addition, of 878 genera retrieved, 92.1 % of the sequences were unique to pyrosequencing. For culture-dependent analysis, plate culturing, plate washing, enrichment, and high-throughput culturing (HTC) methods were applied. Phylogenetic analysis showed that the plate-washing clones formed a cluster devoid of any previously cultured representatives within the family Rhodobacteraceae. One HTC isolate (SF293) fell into the OM182 clade, which was not recovered by other culturing methods described here. By directly comparing the sequences obtained from cultures with those from culture-independent work, we found that only 33% of the culture sequences were identical to those from clone libraries and pyrosequences. This study presents a detailed comparison of common molecular and cultivation techniques available in microbial ecology. As different methods yielded different coverage, we suggest choosing the approach after carefully examining the scientific questions being asked.