Response of aerobic anoxygenic phototrophic bacteria to limitation and availability of organic carbon.

Aerobic Anoxygenic Phototrophic (AAP) bacteria are an important component of freshwater bacterioplankton. They can support their heterotrophic metabolism with energy from light, enhancing their growth efficiency. Based on results from cultures, it was hypothesized that photoheterotrophy provides an advantage under carbon limitation and facilitates access to recalcitrant or low-energy carbon sources. However, verification of these hypotheses for natural AAP communities has been lacking. Here, we conducted whole community manipulation experiments and compared the growth of AAP bacteria under carbon limited and with recalcitrant or low-energy carbon sources under dark and light (near-infrared light, λ>800 nm) conditions to elucidate how they profit from photoheterotrophy. We found that AAP bacteria induce photoheterotrophic metabolism under carbon limitation but they overcompete heterotrophic bacteria when carbon is available. This effect seems to be driven by physiological responses rather than changes at the community level. Interestingly, recalcitrant (lignin) or low-energy (acetate) carbon sources inhibited the growth of AAP bacteria, especially in light. This unexpected observation may have ecosystem-level consequences as lake browning continues. In general, our findings contribute to the understanding of the dynamics of AAP bacteria in pelagic environments.

Tideless estuaries in brackish seas as possible freshwater-marine transition zones for bacteria: the case study of the Vistula river estuary.

Most bacteria are found either in marine or fresh waters and transitions between the two habitats are rare, even though freshwater and marine bacteria co-occur in brackish habitats. Estuaries in brackish, tideless seas could be habitats where the transition of freshwater phylotypes to marine conditions occurs. We tested this hypothesis in the Gulf of Gdansk (Baltic Sea) by comparing bacterial communities from different zones of the estuary, via pyrosequencing of 16S rRNA amplicons. We predicted the existence of a core microbiome (CM, a set of abundant OTUs present in all samples) comprising OTUs consisting of populations specific for particular zones of the estuary. The CMs for the entire studied period consisted of only eight OTUs, and this number was even lower for specific seasons: five in spring, two in summer, and one in autumn and winter. Six of the CM OTUs, and another 21 of the 50 most abundant OTUs consisted of zone-specific populations, plausibly representing micro-evolutionary forces. The presence of up to 15% of freshwater phylotypes from the Vistula River in the brackish Gulf of Gdansk supported our hypothesis, but high dissimilarity between the bacterial communities suggested that freshwater-marine transitions are rare even in tideless estuaries in brackish seas.

A fish-based index for assessing the ecological status of Polish transitional and coastal waters.

Fish assemblages are considered indicators of aquatic ecosystem quality. Based on how fish communities respond to anthropogenic pressures, we developed a multimetric fish index for evaluating the health of both coastal and transitional waters. Fish data were collected along the Polish coast in the years 2011, 2013 and 2014 using different types of gear. Redundancy analysis showed that the most important environmental factor affecting fish community was salinity. Responses to anthropogenic disturbances of 20 candidate metrics were tested by generalized linear models, taking into account salinity, sampling protocol and the proxy of human pressures described by the Baltic Sea Impact Index (BSII). Five selected metrics were combined in a Multimetric Index, which showed negative significant correlation with BSII. The index presented herein appeared to be a good tool for assessing the ecological state of highly impacted Polish transitional and coastal areas and complies with the Water Framework Directive requirements.

Distribution of small phytoflagellates along an Arctic fjord transect.

Phytoflagellates <10 µm substantially contribute to the abundance, biomass and primary production in polar waters, but information on the distribution of specific groups is scarce. We applied catalysed reporter deposition-fluorescence in situ hybridization to investigate the distribution of total phytoflagellates and of eight specific groups along a 100 km transect west off Kongsfjorden (Spitsbergen) from 29 to 31 July 2010. Phytoflagellates contributed to >75% of the depth-integrated abundance and biomass of total eukaryotes <10 µm at all stations. Their depth-integrated abundance and biomass decreased along the transect from 1.5 × 10(12) cells m(-2) (6.6 × 10(12) pgC m(-2) ) at the outermost station to 1.7 × 10(10) cells m(-2) (4.7 × 10(10) pgC m(-2) ) at the innermost station. Chlorophytes contributed to the total abundance of phytoflagellates with a range from 13% to 87% (0.7-30.5 × 10(3) cells ml(-1) ), and predominated in open waters. The contribution of haptophytes was < 1-38% (10-4500 cells ml(-1) ). The other groups represented <10%. The temperature and salinity positively correlated with the total abundance of phytoflagellates, chlorophytes, haptophytes, bolidophytes and pelagophytes. Cryptophytes, pedinellids and pavlovophytes were negatively associated with the nutrient concentrations. The community composition of phytoflagellates changed along the transect, which could have implications on food web dynamics and biogeochemical cycles between the open ocean environment and Kongsfjorden investigated here.

Influence of the Escherichia coli oxyR gene function on lambda prophage maintenance.

In Escherichia coli hosts, hydrogen peroxide is one of the factors that may cause induction of lambda prophage. Here, we demonstrate that H2O2-mediated lambda prophage induction is significantly enhanced in the oxyR mutant host. The mRNA levels for cI gene expression were increased in a lambda lysogen in the presence of H2O2. On the other hand, stimulation of the p(M) promoter by cI857 overproduced from a multicopy plasmid was decreased in the DeltaoxyR mutant in the presence of H2O2 but not under normal growth conditions. The purified OxyR protein did bind specifically to the p(M) promoter region. This binding impaired efficiency of interaction of the cI protein with the OR3 site, while stimulating such a binding to OR2 and OR1 sites, in the regulatory region of the p(M) promoter. We propose that changes in cI gene expression, perhaps in combination with moderately induced SOS response, may be responsible for enhanced lambda prophage induction by hydrogen peroxide in the oxyR mutant. Therefore, OxyR seems to be a factor stimulating lambda prophage maintenance under conditions of oxidative stress. This proposal is discussed in the light of efficiency of induction of lambdoid prophages bearing genes coding for Shiga toxins.

Plasmids derived from Gifsy-1/Gifsy-2, lambdoid prophages contributing to the virulence of Salmonella enterica serovar Typhimurium: implications for the evolution of replication initiation proteins of lambdoid phages and enterobacteria.

Gifsy-1 and Gifsy-2 are lambdoid prophages which contribute to the virulence of Salmonella enterica serovar Typhimurium. The nucleotide sequence of the replication region of both prophages is identical, and similar in organization to the replication region of bacteriophage lambda. To investigate the replication of the Gifsy phages and the relationship between Gifsy and host chromosome replication, a plasmid which contained all the genes and regulatory sequences required for autonomous replication in bacterial cells was constructed. This plasmid, pGifsy, was stably maintained in Escherichia coli cells. The helicase loader of the Gifsy phages is very similar to the DnaC protein of the host, a feature characteristic of a large group of prophages common in the sequenced genomes of pathogenic enterobacteria. This DnaC-like protein showed no similarity to the helicase loader of bacteriophage lambda and closely related phages. Interestingly, unlike plasmids derived from bacteriophage lambda (lambda plasmids), pGifsy did not require a gene encoding the putative helicase loader for replication, although deletion of this gene resulted in a decrease in plasmid copy number. Under these conditions, it was shown that the plasmid utilized the helicase loader coded by the host. On the other hand, the viral protein could not substitute for DnaC in bacterial chromosome replication. The results of the current study support the hypothesis that the enterobacterial helicase loader is of viral origin. This hypothesis explains why the gene for DnaC, the protein central to both replication initiation and replication restart in E. coli, is present in the genomes of Escherichia, Shigella, Salmonella and Buchnera, but not in the genomes of related enterobacteria.