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Bacteria play a key role in the planetary carbon cycle partly because they rapidly assimilate labile dissolved organic matter (DOM) in the ocean. However, knowledge of the molecular mechanisms at work when bacterioplankton metabolize distinct components of the DOM pool is still limited. We, therefore, conducted seawater culture enrichment experiments with ecologically relevant DOM, combining both polymer and monomer model compounds for distinct compound classes. This included carbohydrates (polysaccharides vs. monosaccharides), proteins (polypeptides vs. amino acids), and nucleic acids (DNA vs. nucleotides). We noted pronounced changes in bacterial growth, activity, and transcription related to DOM characteristics. Transcriptional responses differed between compound classes, with distinct gene sets (“core genes”) distinguishing carbohydrates, proteins, and nucleic acids. Moreover, we found a strong divergence in functional transcription at the level of particular monomers and polymers (i.e., the condensation state), primarily in the carbohydrates and protein compound classes. These specific responses included a variety of cellular and metabolic processes that were mediated by distinct bacterial taxa, suggesting pronounced functional partitioning of organic matter. Collectively, our findings show that two important facets of DOM, compound class and condensation state, shape bacterial gene expression, and ultimately select for distinct bacterial (functional) groups. This emphasizes the interdependency of marine bacteria and labile carbon compounds for regulating the transformation of DOM in surface waters.

Bacteria play a key role in the planetary carbon cycle partly because they rapidly assimilate labile dissolved organic matter (DOM) in the ocean. However, knowledge of the molecular mechanisms at work when bacterioplankton metabolize distinct components of the DOM pool is still limited. We, therefore, conducted seawater culture enrichment experiments with ecologically relevant DOM, combining both polymer and monomer model compounds for distinct compound classes. This included carbohydrates (polysaccharides vs. monosaccharides), proteins (polypeptides vs. amino acids), and nucleic acids (DNA vs. nucleotides). We noted pronounced changes in bacterial growth, activity, and transcription related to DOM characteristics. Transcriptional responses differed between compound classes, with distinct gene sets ("core genes") distinguishing carbohydrates, proteins, and nucleic acids. Moreover, we found a strong divergence in functional transcription at the level of particular monomers and polymers (i.e., the condensation state), primarily in the carbohydrates and protein compound classes. These specific responses included a variety of cellular and metabolic processes that were mediated by distinct bacterial taxa, suggesting pronounced functional partitioning of organic matter. Collectively, our findings show that two important facets of DOM, compound class and condensation state, shape bacterial gene expression, and ultimately select for distinct bacterial (functional) groups. This emphasizes the interdependency of marine bacteria and labile carbon compounds for regulating the transformation of DOM in surface waters. [ABSTRACT FROM AUTHOR]

Chrysene is a high molecular weight (HMW), polycyclic aromatic hydrocarbon (PAH) known for its recalcitrance and carcinogenic properties and sparsely soluble (0.003 mg/L) in aqueous medium. Due to these refractory properties, bioavailability of chrysene is very low and therefore is persistence in the environment escaping the metabolism by microorganisms. However, few bacterial and fungal strains are reported to degrade chrysene, but with lower efficiency, requiring additional/extraneous carbon sources (co-substrates) for it’s complete mineralization. In this study, development, enrichment and characterization of bacterial consortium ASDC, consisting of Rhodococcus sp., ASDC1; Bacillus sp. ASDC2; and Burkholderia sp. ASDC3 were reported. Chrysene was utilized as a sole source of carbon and energy by the consortium, having maximum degradation rate of 1.5 mg/L/day and maximum growth rate of 0.125/h, under optimized conditions of pH 7.0, 37°C under aeration of 150 rpm on gyrating shaking. Chrysene degradation was unaffected in presence of other PAHs like pyrene, fluoranthene, naphthalene, phenanthrene, benzene, toluene and xylene, individually as well as in mixture. The results revealed that peptone, ammonium nitrate, sodium succinate have enhanced the chrysene degradation rate during first 24 h of experimentation, which was later on inhibited with increase in incubation time. The chrysene degradation was inhibited by mercury even at lower concentration (1 mM). The results also revealed that SDS has enhanced its degradation by 5.2-fold for initial 24 h of growth, but with increasing in the incubation period, it decreases by 1.2-fold on 7th day of experimentation. The HPLC studies suggested that chrysene was degraded through phthalic acid pathway by the consortium ASDC and the stoichiometric measurements indicated the complete mineralization of chrysene. The flask scale results were validated at simulated microcosm models, where enriched consortium ASDC exhibited maximum degradation (96%) in polluted, non-sterile soil sediment, indicating that consortial strains along with indigenous metabolism showed synergistic metabolism for degradation of chrysene. Thus, the above study revealed the useful enrichment of bacterial community for synergistic degradation of PAHs (chrysene) which could be further exploited for in situ remediation of PAH contaminated sites.

Plant growth and productivity depend on the interactions of the plant with the associated rhizosphere microbes. Rhizosphere protists play a significant role in this respect: considerable efforts have been made in the past to reveal the impact of protist-bacteria interactions on the remobilization of essential nutrients for plant uptake, or the grazing induced changes on plant-growth promoting bacteria and the root-architecture. However, the metabolic responses of plants to the presence of protists or to protist-bacteria interactions in the rhizosphere have not yet been analyzed. Here we studied in controlled laboratory experiments the impact of bacterivorous protists in the rhizosphere on maize plant growth parameters and the bacterial community composition. Beyond that we investigated the induction of plant biochemical responses by separately analyzing above- and below-ground metabolite profiles of maize plants incubated either with a soil bacterial inoculum or with a mixture of soil bacteria and bacterivorous protists. Significantly distinct leaf and root metabolite profiles were obtained from plants which grew in the presence of protists. These profiles showed decreased levels of a considerable number of metabolites typical for the plant stress reaction, such as polyols, a number of carbohydrates and metabolites connected to phenolic metabolism. We assume that this decrease in plant stress is connected to the grazing induced shifts in rhizosphere bacterial communities as shown by distinct T-RFLP community profiles. Protist grazing had a clear effect on the overall bacterial community composition, richness and evenness in our microcosms. Given the competition of plant resource allocation to either defense or growth, we propose that a reduction in plant stress levels caused directly or indirectly by protists may be an additional reason for corresponding positive effects on plant growth.

Chrysene is a high molecular weight (HMW), polycyclic aromatic hydrocarbon (PAH) known for its recalcitrance and carcinogenic properties and sparsely soluble (0.003 mg/L) in aqueous medium. Due to these refractory properties, bioavailability of chrysene is very low and therefore is persistence in the environment escaping the metabolism by microorganisms. However, few bacterial and fungal strains are reported to degrade chrysene, but with lower efficiency, requiring additional/extraneous carbon sources (co-substrates) for it’s complete mineralization. In this study, development, enrichment and characterization of bacterial consortium ASDC, consisting of Rhodococcus sp., ASDC1; Bacillus sp. ASDC2; and Burkholderia sp. ASDC3 were reported. Chrysene was utilized as a sole source of carbon and energy by the consortium, having maximum degradation rate of 1.5 mg/L/day and maximum growth rate of 0.125/h, under optimized conditions of pH 7.0, 37°C under aeration of 150 rpm on gyrating shaking. Chrysene degradation was unaffected in presence of other PAHs like pyrene, fluoranthene, naphthalene, phenanthrene, benzene, toluene and xylene, individually as well as in mixture. The results revealed that peptone, ammonium nitrate, sodium succinate have enhanced the chrysene degradation rate during first 24 h of experimentation, which was later on inhibited with increase in incubation time. The chrysene degradation was inhibited by mercury even at lower concentration (1 mM). The results also revealed that SDS has enhanced its degradation by 5.2-fold for initial 24 h of growth, but with increasing in the incubation period, it decreases by 1.2-fold on 7th day of experimentation. The HPLC studies suggested that chrysene was degraded through phthalic acid pathway by the consortium ASDC and the stoichiometric measurements indicated the complete mineralization of chrysene. The flask scale results were validated at simulated microcosm models, where enriched consortium ASDC exhibited maximum degradation (96%) in polluted, non-sterile soil sediment, indicating that consortial strains along with indigenous metabolism showed synergistic metabolism for degradation of chrysene. Thus, the above study revealed the useful enrichment of bacterial community for synergistic degradation of PAHs (chrysene) which could be further exploited for in situ remediation of PAH contaminated sites. [ABSTRACT FROM AUTHOR]

Plant growth and productivity depend on the interactions of the plant with the associated rhizosphere microbes. Rhizosphere protists play a significant role in this respect: considerable efforts have been made in the past to reveal the impact of protist-bacteria interactions on the remobilization of essential nutrients for plant uptake, or the grazing induced changes on plant-growth promoting bacteria and the rootarchitecture. However, the metabolic responses of plants to the presence of protists or to protist-bacteria interactions in the rhizosphere have not yet been analyzed. Here we studied in controlled laboratory experiments the impact of bacterivorous protists in the rhizosphere on maize plant growth parameters and the bacterial community composition. Beyond that we investigated the induction of plant biochemical responses by separately analyzing above- and below-ground metabolite profiles of maize plants incubated either with a soil bacterial inoculum or with a mixture of soil bacteria and bacterivorous protists. Significantly distinct leaf and root metabolite profiles were obtained from plants which grew in the presence of protists. These profiles showed decreased levels of a considerable number of metabolites typical for the plant stress reaction, such as polyols, a number of carbohydrates and metabolites connected to phenolic metabolism. We assume that this decrease in plant stress is connected to the grazing induced shifts in rhizosphere bacterial communities as shown by distinct T-RFLP community profiles. Protist grazing had a clear effect on the overall bacterial community composition, richness and evenness in our microcosms. Given the competition of plant resource allocation to either defense or growth, we propose that a reduction in plant stress levels caused directly or indirectly by protists may be an additional reason for corresponding positive effects on plant growth. [ABSTRACT FROM AUTHOR]

The aim of this study was to investigate selective pressure of antibiotics on antibiotic resistance genes (ARGs) and bacterial communities in manure-polluted aquatic environment. Three treatment groups were set up in freshwater-sediment microcosms: tetracyclines group, sulfonamides group and fluoroquinolones group. Sediment and water samples were collected on day 14 after treatment. Antibiotic concentrations, ARGs abundances and bacterial community composition were analyzed. Antibiotic concentrations were determined by ultra-performance liquid chromatography-electrospray tandem mass spectrometry. ARGs abundances were quantified by real time quantitative PCR. Bacterial community composition was analyzed based on amplicon sequencing. Of the three classes of antibiotics analyzed in the treatment groups, accumulation amounts were tetracyclines> fluoroquinolone> sulfonamides in the sediment samples, while they were sulfonamides> fluoroquinolone> tetracyclines in the water samples. In the treatment groups, the relative abundances of some tet resistance genes (tet(W) and tet(X)) and plasmid-mediated quinolone resistance (PMQR) genes (oqx(B) and aac(6’)-Ib) in sediment samples were significantly higher than those in the paired water samples. Tetracyclines significantly selected the bacterial classes including Gammaproteobacteria, Clostridia, and the genera including Salmonella, Escherichia/Shigella, Clostridium, Stenotrophomonas in sediment samples. The significant selection on bacterial communities posed by sulfonamides and fluoroquinolones was also observed. The results indicated that sediment may supply an ideal setting for maintenance and persistence of tet resistance genes (tet(W) and tet(X)) and PMQR genes (oqx(B) and aac(6’)-Ib) under antibiotic pollution. The results also highlighted that antibiotics significantly selected specific bacterial communities including the taxa associated with opportunistic pathogens.

Water availability is the main limiting factor in arid soils; however few studies have examined the effects of drying and rewetting on nitrifiers from these environments. The effect of water availability on the diversity of ammonia-oxidizing bacteria (AOB) and archaea (AOA) from a semiarid soil of the Chilean sclerophyllous matorral was determined by microcosm assays. The addition of water every 14 days to reach 60% of the WHC significantly increased nitrate content in rewetted soil microcosms (p

The distribution of neutrophilic microbial iron oxidation is mainly determined by local gradients of oxygen, light, nitrate and ferrous iron. In the anoxic top part of littoral freshwater lake sediments, nitrate-reducing and phototrophic Fe(II)-oxidizers compete for the same e- donor; reduced iron. It is not yet understood how these microbes co-exist in the sediment and what role they play in the Fe cycle. We show that both metabolic types of anaerobic Fe(II)-oxidizing microorganisms are present in the same sediment layer directly beneath the oxic-anoxic sediment interface. The photoferrotrophic MPNs counted 3.4•105 cells•g-1 and the autotrophic and mixotrophic nitrate-reducing Fe(II)-oxidizers totalled 1.8•104 and 4.5•104 cells•g-1 dry weight sediment, respectively. To distinguish between the two microbial Fe(II) oxidation processes and assess their individual contribution to the sedimentary Fe cycle, littoral lake sediment was incubated in microcosm experiments. Nitrate-reducing Fe(II)-oxidizing bacteria exhibited a higher maximum Fe(II) oxidation rate per cell, in both pure cultures and microcosms, than photoferrotrophs. In microcosms, photoferrotrophs instantly started oxidizing Fe(II), whilst nitrate-reducing Fe(II)-oxidizers showed a significant lag-phase during which they probably use organics as e- donor before initiating Fe(II) oxidation. This suggests that they will be outcompeted by phototrophic Fe(II)-oxidizers during optimal light conditions; as phototrophs deplete Fe(II) before nitrate-reducing Fe(II)-oxidizers start Fe(II) oxidation. Thus, the co-existence of the two anaerobic Fe(II)-oxidizers may be possible due to a niche space separation in time by the day-night cycle, where nitrate-reducing Fe(II)-oxidizers oxidize Fe(II) during darkness and phototrophs play a dominant role in Fe(II) oxidation during daylight. Furthermore, metabolic flexibility of Fe(II)-oxidizing microbes may play a paramount role in the conservation of the sedimentary Fe cycle.

Understanding how Listeria monocytogenes , the causative agent of listeriosis, adapts to the environment is crucial. Adaptation to new matrices requires regulation of gene expression. To determine how the pathogen adapts to lagoon effluent and soil, two matrices where L. monocytogenes has been isolated, we compared the transcriptomes of L. monocytogenes CIP 110868 20 min and 24 h after its transfer to effluent and soil extract. Results showed major variations in the transcriptome of L. monocytogenes in the lagoon effluent but only minor modifications in the soil. In both the lagoon effluent and in the soil, genes involved in mobility and chemotaxis and in the transport of carbohydrates were the most frequently represented in the set of genes with higher transcript levels, and genes with phage-related functions were the most represented in the set of genes with lower transcript levels. A modification of the cell envelop was only found in the lagoon environment. Finally, the differential analysis included a large proportion of regulators, regulons, and ncRNAs.