Frequency and Diversity of Nitrate Reductase Genes among Nitrate-Dissimilating Pseudomonas in the Rhizosphere of Perennial Grasses Grown in Field Conditions

A total of 1246 Pseudomonas strains were isolated from the rhizosphere of two perennial grasses (Lolium perenne and Molinia coerulea) with different nitrogen requirements. The plants were grown in their native soil under ambient and elevated atmospheric CO2 content (pCO2) at the Swiss FACE (Free Air CO2 Enrichment) facility. Root-, rhizosphere-, and non-rhizospheric soil-associated strains were characterized in terms of their ability to reduce nitrate during an in vitro assay and with respect to the genes encoding the membrane-bound (named NAR) and periplasmic (NAP) nitrate reductases so far described in the genus Pseudomonas. The diversity of corresponding genes was assessed by PCR-RFLP on narG and napA genes, which encode the catalytic subunit of nitrate reductases. The frequency of nitrate-dissimilating strains decreased with root proximity for both plants and was enhanced under elevated pCO2 in the rhizosphere of L. perenne. NAR (54% of strains) as well as NAP (49%) forms were present in nitrate-reducing strains, 15.5% of the 439 strains tested harbouring both genes. The relative proportions of narG and napA detected in Pseudomonas strains were different according to root proximity and for both pCO2 treatments: the NAR form was more abundant close to the root surface and for plants grown under elevated pCO2. Putative denitrifiers harbored mainly the membrane-bound (NAR) form of nitrate reductase. Finally, both narG and napA sequences displayed a high level of diversity. Anyway, this diversity was correlated neither with the root proximity nor with the pCO2 treatmen

An Assessment of Beaked Redfish (S. mentella and S. fasciatus) in NAFO Division 3M (at times when natural mortality is driven stock dynamics and fishing mortality reference points are useless to scientific advice)

The 3M redfish assessment is focused on the beaked redfish, regarded as a management unit composed of two populations from two very similar species: the Flemish Cap S. mentella and S. fasciatus. The reason for this approach is the historical dominance of this group in the 3M redfish commercial catch until 2005. However a new golden redfish fishery (S. marinus) started on September 2005 on shallower depths of the Flemish Cap bank above 300m, and the Flemish Cap cod fishery reopened in 2010. These new realities implied a revision of catch estimates, in order to split recent redfish commercial catch and by-catch from the major fleets on Div. 3M into golden (S. marinus) and beaked (S. mentella and S. fasciatus) redfish catches. The Extended Survivor Analysis assessment used as tuning file the 1989-2014 EU survey abundance at age matrix included in a revised input framework. Continuing pressure over Flemish Cap redfish stocks by cod predation, at levels higher, or much higher, than the levels prior to 2006 lead to higher natural mortalities since then. Natural mortality have been tuned to survey at age data 2006 onwards by the sensitivity analysis preceding each assessment, and on 2013-2104 has a best estimate at slightly higher level from previous years. A 2015-2011 retrospective XSA was carried out, confirming that the present assessment is very much in line with their immediate predecessors

Robust estimation of microbial diversity in theory and in practice

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ("Hill diversities"), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.Comment: To be published in The ISME Journal. Main text: 16 pages, 5 figures. Supplement: 16 pages, 4 figure

Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens

<p>Abstract</p> <p>Background</p> <p>The influence of diet on intestinal microflora has been investigated mainly using conventional microbiological approaches. Although these studies have advanced knowledge on human intestinal microflora, it is imperative that new methods are applied to facilitate scientific progress. Culture-independent molecular fingerprinting method of Polymerase Chain Reaction and Denaturing Gradient Gel Electrophoresis (PCR-DGGE) has been used to study microbial communities in a variety of environmental samples. However, these protocols must be optimized prior to their application in order to enhance the quality and accuracy of downstream analyses. In this study, the relative efficacy of four commercial DNA extraction kits (Mobio Ultra Clean^®Fecal DNA Isolation Kit, M; QIAamp^®DNA Stool Mini Kit, Q; FastDNA^®SPIN Kit, FSp; FastDNA^®SPIN Kit for Soil, FSo) were evaluated. Further, PCR-DGGE technique was also assessed for its feasibility in detecting differences in human intestinal bacterial fingerprint profiles.</p> <p>Method</p> <p>Total DNA was extracted from varying weights of human fecal specimens using four different kits, followed by PCR amplification of bacterial 16S rRNA genes, and DGGE separation of the amplicons.</p> <p>Results</p> <p>Regardless of kit, maximum DNA yield was obtained using 10 to 50 mg (wet wt) of fecal specimens and similar DGGE profiles were obtained. However, kits FSp and FSo extracted significantly larger amounts of DNA per g dry fecal specimens and produced more bands on their DGGE profiles than kits M and Q due to their use of bead-containing lysing matrix and vigorous shaking step. DGGE of 16S rRNA gene PCR products was suitable for capturing the profiles of human intestinal microbial community and enabled rapid comparative assessment of inter- and intra-subject differences.</p> <p>Conclusion</p> <p>We conclude that extraction kits that incorporated bead-containing lysing matrix and vigorous shaking produced high quality DNA from human fecal specimens (10 to 50 mg, wet wt) that can be resolved as bacterial community fingerprints using PCR-DGGE technique. Subsequently, PCR-DGGE technique can be applied for studying variations in human intestinal microbial communities.</p

Fungal community composition and metabolism under elevated CO 2 and O 3

Atmospheric CO 2 and O 3 concentrations are increasing due to human activity and both trace gases have the potential to alter C cycling in forest ecosystems. Because soil microorganisms depend on plant litter as a source of energy for metabolism, changes in the amount or the biochemistry of plant litter produced under elevated CO 2 and O 3 could alter microbial community function and composition. Previously, we have observed that elevated CO 2 increased the microbial metabolism of cellulose and chitin, whereas elevated O 3 dampened this response. We hypothesized that this change in metabolism under CO 2 and O 3 enrichment would be accompanied by a concomitant change in fungal community composition. We tested our hypothesis at the free-air CO 2 and O 3 enrichment (FACE) experiment at Rhinelander, Wisconsin, in which Populus tremuloides , Betula papyrifera , and Acer saccharum were grown under factorial CO 2 and O 3 treatments. We employed extracellular enzyme analysis to assay microbial metabolism, phospholipid fatty acid (PLFA) analysis to determine changes in microbial community composition, and polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE) to analyze the fungal community composition. The activities of 1,4-β-glucosidase (+37%) and 1,4,-β- N -acetylglucosaminidase (+84%) were significantly increased under elevated CO 2 , whereas 1,4-β-glucosidase activity (−25%) was significantly suppressed by elevated O 3 . There was no significant main effect of elevated CO 2 or O 3 on fungal relative abundance, as measured by PLFA. We identified 39 fungal taxonomic units from soil using DGGE, and found that O 3 enrichment significantly altered fungal community composition. We conclude that fungal metabolism is altered under elevated CO 2 and O 3 , and that there was a concomitant change in fungal community composition under elevated O 3 . Thus, changes in plant inputs to soil under elevated CO 2 and O 3 can propagate through the microbial food web to alter the cycling of C in soil.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47711/1/442_2005_Article_249.pd

Climate change goes underground: effects of elevated atmospheric CO2 on microbial community structure and activities in the rhizosphere.

General concern about climate change has led to growing interest in the responses of terrestrial ecosystems to elevated concentrations of CO2 in the atmosphere. Experimentation during the last two to three decades using a large variety of approaches has provided sufficient information to conclude that enrichment of atmospheric CO2 may have severe impact on terrestrial ecosystems. This impact is mainly due to the changes in the organic C dynamics as a result of the effects of elevated CO2 on the primary source of organic C in soil, i.e., plant photosynthesis. As the majority of life in soil is heterotrophic and dependent on the input of plant-derived organic C, the activity and functioning of soil organisms will greatly be influenced by changes in the atmospheric CO2 concentration. In this review, we examine the current state of the art with respect to effects of elevated atmospheric CO2 on soil microbial communities, with a focus on microbial community structure. On the basis of the existing information, we conclude that the main effects of elevated atmospheric CO2 on soil microbiota occur via plant metabolism and root secretion, especially in C3 plants, thereby directly affecting the mycorrhizal, bacterial, and fungal communities in the close vicinity of the root. There is little or no direct effect on the microbial community of the bulk soil. In particular, we have explored the impact of these changes on rhizosphere interactions and ecosystem processes, including food web interactions