Lipids from heterotrophic microbes: advances in metabolism research

Heterotrophic oleaginous microorganisms are capable of producing over 20% of their weight in single cell oils (SCOs) composed of triacylglycerols (TAGs). These TAGs contain fatty acids, such as palmitic, stearic and oleic acids, that are well-suited for biodiesel applications. Although some of these microbes are able to accumulate SCOs while growing on inexpensive agro-industrial biomass, the competition with plant oil resources means that a significant increase in productivity is desired. The present review aims to summarize recent details in lipid metabolism research and engineering (e.g. direct fatty acid ethyl ester production), as well as culture condition optimization and innovations, such as solid-state or semi-solid-state fermentation, that can all contribute to higher productivity and further advancement of the field.     

Oligotrophic properties of heterotrophic bacteria and in situ heterotrophic activity in pelagic seawates

Abstract The distribution of heterotrophic bacteria in polluted coastal and unpolluted pelagic seawaters was studied using a ¹⁴C-MPN method with either five of seven kinds of ¹⁴C-organic compounds as substrates. The total number of heterotrophic bacteria in pelagic waters ranged from 9.2 × 10³ to 5.4. ¢ 10⁴ cell/ml and more than 85% of the heterotrophic bacteria were represented by obligate oligotrophs. In coastal waters, the number of heterotrophs was one order of magnitude higher (av. 3.5 ¢ 10⁵ cells/ml), and eutrophic and facultatively oligotrophic bacteria were predominant. Oligotrophs in pelagic waters had a high specificity for the utilization of amino acids, especially glycine, and acetate-utilizing bacteria were scarce. The in situ maximum uptake rates of glutamate and glycine were much higher than those of glycolate and acetate. Acetate uptake rates were extremely low or not detectable in pelagic waters. The specificity of uptake kinetics is assumed to depend on the existence of obligate oligotrophs as dominant bacteria in pelagic seawater.     

Adaptive genetic traits in pelagic freshwater microbes

Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and ‘Ca. Patescibacteria’.     

Thermal acclimation in widespread heterotrophic soil microbes

Respiration by plants and microorganisms is primarily responsible for mediating carbon exchanges between the biosphere and atmosphere. Climate warming has the potential to influence the activity of these organisms, regulating exchanges between carbon pools. Physiological ‘down‐regulation’ of warm‐adapted species (acclimation) could ameliorate the predicted respiratory losses of soil carbon under climate change scenarios, but unlike plants and symbiotic microbes, the existence of this phenomenon in heterotrophic soil microbes remains controversial. Previous studies using complex soil microbial communities are unable to distinguish physiological acclimation from other community‐scale adjustments. We explored the temperature‐sensitivity of individual saprotrophic basidiomycete fungi growing in agar, showing definitively that these widespread heterotrophic fungi can acclimate to temperature. In almost all cases, the warm‐acclimated individuals had lower growth and respiration rates at intermediate temperatures than cold‐acclimated isolates. Inclusion of such microbial physiological responses to warming is essential to enhance the robustness of global climate‐ecosystem carbon models.     

Fate of starch-containing plastic films exposed in aquatic habitats

Plastic films containing cornstarch (40% dry weight) in combination with polyethylene (PE) and polyethylene-co-acrylic acid (EAA) were exposed to river and pond habitats for up to 60 days. Fourier transform infrared (FTIR) spectroscopic analysis of the starch-plastic films indicated that up to about 40% of starch in the films disappeared after 60 days' exposure. PE and EAA components were unchanged during this period. A diverse microbial biofilm quickly accumulated on each of the plastic films in both environments. Although the amount of biofilm accumulation was greater in the river environment than in the pond environment, there was little quantitative difference in the extent of biofilm formation on plastic films composed of PE, EAA, or starch-PE-EAA in either environment. All three types of plastic films were heavily colonized by a midge-fly larva (Dicrotendipes sp.) by 60 days of exposure in the aquatic environments, but only starch-containing plastic films showed any evidence of physical damage that could have been a result of ingestion of the plastic by the larvae (pond>river), suggesting that, in addition to microbial starch degradation, biodisintegration may also be a significant factor influencing the environmental fate of starch-containing plastics.     

Microbial hitchhikers on microplastics: The exchange of aquatic microbes across distinct aquatic habitats

Microplastics (MPs) have the potential to modify aquatic microbial communities and distribute microorganisms, including pathogens. This poses a potential risk to aquatic life and human health. Despite this, the fate of ‘hitchhiking’ microbes on MPs that traverse different aquatic habitats remains largely unknown. To address this, we conducted a 50-day microcosm experiment, manipulating estuarine conditions to study the exchange of bacteria and microeukaryotes between river, sea and plastisphere using a long-read metabarcoding approach. Our findings revealed a significant increase in bacteria on the plastisphere, including Pseudomonas, Sphingomonas, Hyphomonas, Brevundimonas, Aquabacterium and Thalassolituus, all of which are known for their pollutant degradation capabilities, specifically polycyclic aromatic hydrocarbons. We also observed a strong association of plastic-degrading fungi (i.e., Cladosporium and Plectosphaerella) and early-diverging fungi (Cryptomycota, also known as Rozellomycota) with the plastisphere. Sea MPs were primarily colonised by fungi (70%), with a small proportion of river-transported microbes (1%–4%). The mere presence of MPs in seawater increased the relative abundance of planktonic fungi from 2% to 25%, suggesting significant exchanges between planktonic and plastisphere communities. Using microbial source tracking, we discovered that MPs only dispersed 3.5% and 5.5% of river bacterial and microeukaryotic communities into the sea, respectively. Hence, although MPs select and facilitate the dispersal of ecologically significant microorganisms, drastic compositional changes across distinct aquatic habitats are unlikely.     

Fate of heterotrophic bacteria in Lake Tanganyika (East Africa)

Bacterial mortality was studied using two complementary methods between 2002 and 2004 in the two main basins (north and south) of Lake Tanganyika. The disappearance of radioactivity from the DNA of natural assemblages of bacteria previously labeled with tritiated thymidine was used to estimate the mortality due to grazing by predators (72%) and due to the cell lysis (28%). Measurements of ingestion rate of bacteria by protozoa using fluorescent micro-particles yielded protozoan grazing rates similar to those provided by the thymidine method, and showed that heterotrophic nano-flagellates were responsible for most of the grazing pressure on the bacterial community of the pelagic zone (92-99%). Bacterial cell lysis was the second process involved in bacterial mortality, ranking before ciliate grazing. Overall, bacterial mortality was balanced with bacterial production. With regard to the assessment of the trophic role of bacteria, it was estimated that c. 5-8% of the organic carbon taken up by bacteria was converted into protozoan biomass and was thus available for metazoans.     

Bacterial diversity in a nonsaline alkaline environment: heterotrophic aerobic populations

Heterotrophic populations were isolated and characterized from an alkaline groundwater environment generated by active serpentinization, which results in a Ca(OH)2-enriched, extremely diluted groundwater with pH 11.4. One hundred eighty-five strains were isolated in different media at different pH values during two sampling periods. To assess the degree of diversity present in the environment and to select representative strains for further characterization of the populations, we screened the isolates by using random amplified polymorphic DNA-PCR profiles and grouped them based on similarities determined by fatty acid methyl ester analysis. Phenotypic characterization, determinations of G+C content, phylogenetic analyses by direct sequencing of 16S rRNA genes, and determinations of pH tolerance were performed with the selected isolates. Although 38 different populations were identified and characterized, the vast majority of the isolates were gram positive with high G+C contents and were affiliated with three distinct groups, namely, strains closely related to the species Dietzia natrolimnae (32% of the isolates), to Frigoribacterium/Clavibacter lineages (29% of the isolates), and to the type strain of Microbacterium kitamiense (20% of the isolates). Other isolates were phylogenetically related to strains of the genera Agrococcus, Leifsonia, Kytococcus, Janibacter, Kocuria, Rothia, Nesterenkonia, Citrococcus, Micrococcus, Actinomyces, Rhodococcus, Bacillus, and Staphylococcus. Only five isolates were gram negative: one was related to the Sphingobacteria lineage and the other four were related to the alpha-Proteobacteria lineage. Despite the pH of the environment, the vast majority of the populations were alkali tolerant, and only two strains were able to grow at pH 11.     

Some genetic traits in Solomon island populations. I. Introduction: people and habitats

To introduce a set of genetic studies among Solomon Islanders, four tribal groups on Bougainville and Malaita Islands are described. They were observed in 1966 and 1968 by social anthropologists and biomedical scientists from Harvard University. The groups varied in habitat and way of life from fishermen living on artificial islets in a saltwater lagoon (the Lau, on Malaita) to shifting agriculturists (the Nasioi, on Bougainville, and the Kwaio and Baegu, on Malaita). The Nasioi were darker than the Malaitans and spoke a non-Austronesian rather than a Melanesian language; they were also more Westernized. Coverage of residents in designated hamlets ranged from 78% to over 95%. In all, 1,626 persons were studied: 256 Nasioi, 443 Kwaio, 442 Lau, and 485 Baegu. Genetic differences have been found between the Nasioi and the Malaitans, and between the Lau and the other Malaitans.     

Role of heterotrophic bacteria in promoting N2 fixation byAnabaena in aquatic habitats

Anabaena species are commonly colonized by bacteria, especially during N₂-fixing blooms. Generally these associations do not represent bacterial attack on algal hosts. Instead, the algal N₂-fixing capabilities are increased in the presence of the bacteria. Possible mechanisms promoting the mutual growth of algae and attached bacteria were investigated by observing specific sites of bacterial attachment, by noting reduced microzones created by the bacteria, and by locating sites of bacterial uptake of organics representative of algal excretion products.Attached bacteria show preference for typical algal excretion products and their growth is enhanced by such products. In return, enhancement of algal nitrogenase activity occurs when bacteria create O₂-consuming microzones around the nitrogenase-bearing heterocysts.     

Ecosystem engineers in the pelagic realm: alteration of habitat by species ranging from microbes to jellyfish

Ecosystem engineers are species that alter the physical environment in ways that create new habitat or change the suitability of existing habitats for themselves or other organisms. In marine systems, much of the focus has been on species such as corals, oysters, and macrophytes that add physical structure to the environment, but organisms ranging from microbes to jellyfish and finfish that reside in the water column of oceans, estuaries, and coastal seas alter the chemical and physical environment both within the water column and on the benthos. By causing hypoxia, changing light regimes, and influencing physical mixing, these organisms may have as strong an effect as species that fall more clearly within the classical category of ecosystem engineer. In addition, planktonic species, such as jellyfish, may indirectly alter the physical environment through predator-mediated landscape structure. By creating spatial patterns of habitats that vary in their rates of mortality due to predation, planktonic predators may control spatial patterns and abundances of species that are the direct creators or modifiers of physical habitat.     

Longitudinal differentiation among pelagic populations in a planktic foraminifer

Evolutionary processes in marine plankton have been assumed to be dependent on the oceanic circulation system, which transports plankton between populations in marine surface waters. Gene flow facilitated by oceanic currents along longitudinal gradients may efficiently impede genetic differentiation of pelagic populations in the absence of confounding marine environmental effects. However, how responsible oceanic currents are for the geographic distribution and dispersal of plankton is poorly understood. We examined the phylogeography of the planktic foraminifer Pulleniatina obliquiloculata in the Indo-Pacific Warm Pool (IPWP) by using partial small subunit ribosomal DNA (SSU rDNA) sequences. We found longitudinal clines in the frequencies of three distinct genetic types in the IPWP area. These frequencies were correlated with environmental factors that are characteristic of three water masses in the IPWP. Noteworthy, populations inhabiting longitudinally distant water masses at the Pacific and Indian sides of the IPWP were genetically different, despite transportation of individuals via oceanic currents. These results demonstrate that populations of pelagic plankton have diverged genetically among different water masses within a single climate zone. Changes of the oceanic circulation system could have impacted the geographic patterns of dispersal and divergence of pelagic plankton.     

Piscivore diet response to a collapse in pelagic prey populations

Pelagic fish populations in the upper San Francisco Estuary have experienced significant declines since the turn of the century; a pattern known as the pelagic organism decline (POD). This study investigated food habits of piscivorous fishes over two consecutive fall seasons following the decline of pelagic fish prey. Specifically, this study addressed the contribution of pelagic versus benthic prey to piscivorous fish diets, including the frequency of predation on special-status pelagic species, and the spatial variability in prey consumption. The piscivore community was dominated by Striped Bass and also included small numbers of Sacramento Pikeminnow and Largemouth Bass. Overall, pelagic prey items contributed less than 10% of the diet by weight in both years, whereas pre-POD studies gleaned from the literature found contributions of 39–100%, suggesting a major switch from pelagic to benthic prey resources. Between-year variation in piscivore diets reflected differences in environmental conditions associated with variation in freshwater outflow. No special status fish species were detected in any of the piscivore stomachs examined. The consequences of this pelagic to benthic diet shift warrants further investigation to understand its ecological relevance.     

Sampling characteristics of two methods for capturing age-0 fish in pelagic lake habitats

For the capture of rapidly developing and fast growing age-0 Perca fluviatilis , a sampling precision of <0·2 could be achieved with both push-netting and purse seining. Night catches obtained from purse seining showed predominantly and sometimes significantly higher densities. The push-net system was appropriate for capturing newly hatched larvae and juveniles up to c. 30 mm L_T. The small purse seine was appropriate for fish of 14–30 mm. For perch >30 mm, a 120×5 m purse seine was most suitable.     

不同生境条件下羊草种群无性系和有性生殖特征的比较研究

比较研究了东北草原不同生境条件下4个羊草种群无性系和有性生殖数量特征的差异,结果表明,由于各种群所处立地的资源差异(特别是土壤水分),导致各种群在无性系(包括营养枝和根茎芽密度)和有性生殖(生殖枝密度、生殖枝分化率、生殖贡献)等数量特征方面差异显著,尤其在低平原种群与沙丘种群之间最为显著.与沙丘种群相比,低平原种群营养枝平均密度高50%;根茎芽平均密度高30%以上;生殖枝密度平均值高200%以上.     

拟环纹豹蛛种群遗传多样性与其生境的关系

对分布于我国中南、西南和海南岛8个不同生境的拟环纹豹蛛种群进行RAPD分析.筛选出10对引物扩增出清晰稳定的200～2 500 bp片段84条,其中多态性片段62条(占73.8%).表明种群存在明显多态现象.Shannon指数、相似系数和遗传距离测定以及聚类分析的结果表明：拟环纹豹蛛种群总的遗传多样性指数为0.5177,而且种群内遗传变异（64.24%)大于种群间（35.76%）;8个狼蛛种群平均遗传距离为0.2426,变异范围为0.0753～0.3725,表明8个种群由于所处生境条件不同而产生了一定的适应性变异.多元回归统计结果表明,制约拟环纹豹蛛成为稻田优势种的主要因子是年平均气温和农药的长期施用.     

Flower size variation in Rosmarinus officinalis: individuals, populations and habitats

BACKGROUND AND AIMS: Flowers are relatively invariant organs within species, but quantitative variation often exists among conspecifics. These variations represent the raw material that natural selection can magnify, eventually resulting in morphological divergence and diversification. This paper investigates floral variability in Rosmarinus officinalis, a Mediterranean shrub. METHODS: Nine populations were selected in three major southern Spanish habitats (coast, lowland and mountains) along an elevation gradient. Flower samples from randomly chosen plants were collected from each population, and a total of 641 flowers from 237 shrubs were weighed while still fresh to the nearest 0.1 mg. Leaves from the same plants were also measured. Variations among habitats, sites and plants were explored with general linear model ANOVA. Leaf-flower covariation was also investigated. KEY RESULTS: Most (58%) mass in flowers was accounted for by the corolla, whose linear dimensions correlated directly with flower mass. Averaged over plants, the mass of a flower varied between 12 mg and 38 mg. Habitat, site (within habitat) and shrub identity had significant effects on mass variance. Flowers from the coast were the smallest (17 mg) and those from the mountains the largest (25 mg on average). A pattern of continuously increasing flower size with elevation emerged which was largely uncoupled from the geographical pattern of leaf size variation. CONCLUSIONS: As regards flower size, a great potential to local differentiation exists in Rosmarinus. Observed divergences accord with a regime of large-bodied pollinator selection in the mountains, but also with resource-cost hypotheses on floral evolution that postulate that reduced corollas are advantageous under prevailingly stressful conditions.