Shifts in alkane-degrading bacteria genotypes during bioremediation of a vegetated coastal soil

The effect of plants (milo, oleander and buffelgrass) and hexadecane (1 g/kg of soil) on the diversity of hexadecane-degraders in a coastal soil was investigated. Hexadecane was rapidly degraded during the first 56 days. Its depletion was not plant-enhanced but was slightly retarded by milo and buffelgrass. The diversity of the dominant cultured hexadecane-degrading bacteria was based on sequencing of the V6-8 region of 16S rDNA. On day 0, Alphaproteobacteria prevailed. By day 56, Gammaproteobacteria dominated the contaminated samples whereas similar numbers of Alphaproteobacteria and Gammaproteobacteria genotypes occurred in the uncontaminated samples. Bacteria related to Alcanivorax, a specialized alkane-degrading marine bacterium, were found in all contaminated samples except for buffelgrass rhizospheres, which solely harbored Pseudomonas indica. On day 114, when hexadecane was highly depleted in the contaminated treatments, similar numbers of Alpha- and Gammaproteobacteria genotypes occurred in contaminated and uncontaminated samples. At this stage Alcanivorax had virtually disappeared. Thus in this coastal soil the prevalence of the alkane-dependent Alcanivorax may be a useful indicator of bioremediation progress provided the plant cover favors the dominance of Alcanivorax.     

Dispersal strategies shape persistence and evolution of human gut bacteria

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Changes in the properties of oily gray forest soil during biological reclamation

Biological reclamation of gray forest soil severely contaminated by separator oil using Bacispecin was demonstrated. Agrophysical, agrochemical, physicochemical, and biological properties of the soil were restored in the plow layer during the reclamation.Translated from Izvestiya Akademii Nauk, Seriya Biologicheskaya, No. 1, 2005, pp. 109–115.Original Russian Text Copyright © 2005 by Suleimanov, Gabbasova, Sitdikov.     

Climate change alters ecological strategies of soil bacteria

The timing and magnitude of rainfall events are expected to change in future decades, resulting in longer drought periods and larger rainfall events. Although microbial community composition and function are both sensitive to changes in rainfall, it is unclear whether this is because taxa adopt strategies that maximise fitness under new regimes. We assessed whether bacteria exhibited phylogenetically conserved ecological strategies in response to drying‐rewetting, and whether these strategies were altered by historical exposure to experimentally intensified rainfall patterns. By clustering relative abundance patterns, we identified three discrete ecological strategies and found that tolerance to drying‐rewetting increased with exposure to intensified rainfall patterns. Changes in strategy were primarily due to changes in community composition, but also to strategy shifts within taxa. These moisture regime‐selected ecological strategies may be predictable from disturbance history, and are likely to be linked to traits that influence the functional potential of microbial communities.     

Recent insights in microbial exopolysaccharide biosynthesis and engineering strategies

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A crucial role for exopolysaccharide modification in bacterial biofilm formation, immune evasion, and virulence

Biofilms play an important role in many chronic bacterial infections. Production of an extracellular mixture of sugar polymers called exopolysaccharide is characteristic and critical for biofilm formation. However, there is limited information about the mechanisms involved in the biosynthesis and modification of exopolysaccharide components and how these processes influence bacterial pathogenesis. Staphylococcus epidermidis is an important human pathogen that frequently causes persistent infections by biofilm formation on indwelling medical devices. It produces a poly-N-acetylglucosamine molecule that emerges as an exopolysaccharide component of many bacterial pathogens. Using a novel method based on size exclusion chromatography-mass spectrometry, we demonstrate that the surface-attached protein IcaB is responsible for deacetylation of the poly-N-acetylglucosamine molecule. Most likely due to the loss of its cationic character, non-deacetylated poly-acetylglucosamine in an isogenic icaB mutant strain was devoid of the ability to attach to the bacterial cell surface. Importantly, deacetylation of the polymer was essential for key virulence mechanisms of S. epidermidis, namely biofilm formation, colonization, and resistance to neutrophil phagocytosis and human antibacterial peptides. Furthermore, persistence of the icaB mutant strain was significantly impaired in a murine model of device-related infection. This is the first study to describe a mechanism of exopolysaccharide modification that is indispensable for the development of biofilm-associated human disease. Notably, this general virulence mechanism is likely similar for other pathogenic bacteria and constitutes an excellent target for therapeutic maneuvers aimed at combating biofilm-associated infection.     

Relationship between exopolysaccharide production and protein-tyrosine phosphorylation in gram-negative bacteria

The phosphorylation of proteins at tyrosine residues is known to play a key role in the control of numerous fundamental processes in animal systems. In contrast, the biological significance of protein-tyrosine phosphorylation in bacteria, which has only been recognised recently, is still unclear. Here, we have analysed the role in Escherichia coli cells of an autophosphorylating protein-tyrosine kinase, Wzc, and a phosphotyrosine-protein phosphatase, Wzb, by performing knock-out experiments on the corresponding genes, wzc and wzb, and looking at the metabolic consequences induced. The results demonstrate that the phosphorylation of Wzc, as regulated by Wzb, is directly connected with the production of a particular capsular polysaccharide, colanic acid. Thus, when Wzc is phosphorylated on tyrosine, no colanic acid is synthesised by bacteria, but when dephosphorylated by Wzb, colanic acid is produced. This process is rather specific to the pair of proteins Wzc/Wzb. Indeed, a much lesser effect, if any, on colanic acid synthesis is observed when knock-out experiments are performed on another pair of genes, etk and etp, which also encode respectively a protein-tyrosine kinase, Etk, and a phosphotyrosine-protein phosphatase, Etp, in E. coli. In addition, the analysis of the phosphorylation reaction at the molecular level reveals differences between Gram-negative and Gram-positive bacteria, namely in the number of protein components required for this reaction to occur.     

退化沙质草地开垦和围封过程中的土壤颗粒分形特征

研究了科尔沁退化沙质草地开垦和围封过程中土壤颗粒分形维数的变化特征,以及分形维数与土壤性状的关系.结果表明,不同开垦和围封年限的土壤颗粒分形维数(0～30cm)介于2.387～2.588之间.随着开垦年限的增加,0～15 cm层土壤颗粒分形维数从2.441降至2.387;围封11年后,0～15 cm层土壤颗粒分形维数增加到2.588.15～30 cm层土壤颗粒分形维数无明显变化.土壤颗粒分形维数是反映土壤质地的一个较好指标,重点反映粘粒含量,其次是粉粒含量.分形维数的变化能够很好地表征退化沙质草地土壤的化学、物理和生物学性状的变化趋势,可以作为评价退化沙质草地土壤性状的一个综合指标.     

The emerging role for bacteria in lignin degradation and bio-product formation

The microbial degradation of lignin has been well studied in white-rot and brown-rot fungi, but is much less well studied in bacteria. Recent published work suggests that a range of soil bacteria, often aromatic-degrading bacteria, are able to break down lignin. The enzymology of bacterial lignin breakdown is currently not well understood, but extracellular peroxidase and laccase enzymes appear to be involved. There are also reports of aromatic-degrading bacteria isolated from termite guts, though there are conflicting reports on the ability of termite gut micro-organisms to break down lignin. If biocatalytic routes for lignin breakdown could be developed, then lignin represents a potentially rich source of renewable aromatic chemicals.     

Microtubular determination of cell shape during colony formation by the algaPediastrum

Summary Microtubules, which underlie the plasmalemma of zoospores ofPediastrum at the time of their aggregation to form daughter colonies, determine the shape of individual zoospores, and, as a consequence play a vital role in the patterned arrangement of cells in the colonies. Microtubules are also involved in extension of the characteristic horns on peripheral cells of colonies of this alga. Two densely staining plaques from which microtubules arise, are appressed to the plasmalemma at sites where horns emanate following adhesion of the zoospores. These plaques, which remain at the tips of the developing horns, are apparently microtubule organizing centres (MTOCs). IPC, a drug thought to affect MTOCs, interferes with the normal development of horns and the zoospores fail to aggregate in ordered arrays.     

Changes in N-transforming archaea and bacteria in soil during the establishment of bioenergy crops

Widespread adaptation of biomass production for bioenergy may influence important biogeochemical functions in the landscape, which are mainly carried out by soil microbes. Here we explore the impact of four potential bioenergy feedstock crops (maize, switchgrass, Miscanthus X giganteus, and mixed tallgrass prairie) on nitrogen cycling microorganisms in the soil by monitoring the changes in the quantity (real-time PCR) and diversity (barcoded pyrosequencing) of key functional genes (nifH, bacterial/archaeal amoA and nosZ) and 16S rRNA genes over two years after bioenergy crop establishment. The quantities of these N-cycling genes were relatively stable in all four crops, except maize (the only fertilized crop), in which the population size of AOB doubled in less than 3 months. The nitrification rate was significantly correlated with the quantity of ammonia-oxidizing archaea (AOA) not bacteria (AOB), indicating that archaea were the major ammonia oxidizers. Deep sequencing revealed high diversity of nifH, archaeal amoA, bacterial amoA, nosZ and 16S rRNA genes, with 229, 309, 330, 331 and 8989 OTUs observed, respectively. Rarefaction analysis revealed the diversity of archaeal amoA in maize markedly decreased in the second year. Ordination analysis of T-RFLP and pyrosequencing results showed that the N-transforming microbial community structures in the soil under these crops gradually differentiated. Thus far, our two-year study has shown that specific N-transforming microbial communities develop in the soil in response to planting different bioenergy crops, and each functional group responded in a different way. Our results also suggest that cultivation of maize with N-fertilization increases the abundance of AOB and denitrifiers, reduces the diversity of AOA, and results in significant changes in the structure of denitrification community.     

Electron paramagnetic resonance characterization of the exopolysaccharide layer produced by bacteria

In order to establish a method to characterize the structural heterogeneity of the bacterial surface, research was conducted with a combination of experiments based on electron paramagnetic resonance (EPR) concentration-imaging (CI) and the modeling of translational diffusion with local restrictions. The benefits and drawbacks of this approach are discussed for the Vibrio sp. exopolysaccharide (EPS) layer.     

Distinct growth strategies of soil bacteria as revealed by large-scale colony tracking

Our understanding of microbial ecology has been significantly furthered in recent years by advances in sequencing techniques, but comprehensive surveys of the phenotypic characteristics of environmental bacteria remain rare. Such phenotypic data are crucial for understanding the microbial strategies for growth and the diversity of microbial ecosystems. Here, we describe a high-throughput measurement of the growth of thousands of bacterial colonies using an array of flat-bed scanners coupled with automated image analysis. We used this system to investigate the growth properties of members of a microbial community from untreated soil. The system provides high-quality measurements of the number of CFU, colony growth rates, and appearance times, allowing us to directly study the distribution of these properties in mixed environmental samples. We find that soil bacteria display a wide range of growth strategies which can be grouped into several clusters that cannot be reduced to any of the classical dichotomous divisions of soil bacteria, e.g., into copiotophs and oligotrophs. We also find that, at early times, cells are most likely to form colonies when other, nearby colonies are present but not too dense. This maximization of culturability at intermediate plating densities suggests that the previously observed tendency for high density to lead to fewer colonies is partly offset by the induction of colony formation caused by interactions between microbes. These results suggest new types of growth classification of soil bacteria and potential effects of species interactions on colony growth.     

Shifts in the rhizobiome during consecutive in planta enrichment for phosphate-solubilizing bacteria differentially affect maize P status

Phosphorus (P) is despite its omnipresence in soils often unavailable for plants. Rhizobacteria able to solubilize P are therefore crucial to avoid P deficiency. Selection for phosphate-solubilizing bacteria (PSB) is frequently done in vitro; however, rhizosphere competence is herein overlooked. Therefore, we developed an in planta enrichment concept enabling simultaneous microbial selection for P-solubilization and rhizosphere competence. We used an ecologically relevant combination of iron- and aluminium phosphate to select for PSB in maize (Zea mays L.). In each consecutive enrichment, plant roots were inoculated with rhizobacterial suspensions from plants that had grown in substrate with insoluble P. To assess the plants’ P statuses, non-destructive multispectral imaging was used for quantifying anthocyanins, a proxy for maize’s P status. After the third consecutive enrichment, plants supplied with insoluble P and inoculated with rhizobacterial suspensions showed a P status similar to plants supplied with soluble P. A parallel metabarcoding approach uncovered that the improved P status in the third enrichment coincided with a shift in the rhizobiome towards bacteria with plant growth-promoting and P-solubilizing capacities. Finally, further consecutive enrichment led to a functional relapse hallmarked by plants with a low P status and a second shift in the rhizobiome at the level of Azospirillaceae and Rhizobiaceae.     

中国土壤和植物养分管理现状与改进策略

针对当前我国农业生产面临增肥不增产、土壤养分过量累积、化肥施用过量和养分利用效率下降等重大问题, 本文综述了中国土壤养分与植物营养状况的历史演变和研究进展, 提出中国植物营养科学研究应在跟踪国际科学前沿的同时, 紧密结合中国农业生产实际, 通过大幅度提高养分效率和作物产量为农业可持续发展做出应有的贡献。