Colonisation patterns and vertical movements of stream invertebrates in the interstitial zone: a case study in the Apennines, NW Italy

We examined vertical migration and colonisation patterns of stream macroinvertebrates within the substratum of an Apennine creek in NW Italy. Macrobenthos was sampled at three depths in the streambed (0–5, 5–10, 10–15 cm) by means of artificial baskets filled with natural substratum. We placed 42 traps (5×5×15 cm), i.e. 21 top-opened (T-traps) and 21 bottom-opened (B-traps), each composed of three overlapping baskets (high-H, medium-M and low-L), to evaluate differences in the vertical movements. We also collected Surber samples to compare interstitial assemblages with streambed communities. The multilevel traps yielded 42 taxa, compared with 60 taxa in the natural riverbed. Interstitial traps were rapidly colonised; both taxa richness and organism number increased during the 42-day study period. We found active migration in both vertical directions, but there were more invertebrates in the top-opened traps than in the bottom-opened traps. In the T-traps the most colonised baskets were those placed at the H level, while in the B-traps the L level baskets were more rapidly colonised. The interstitial assemblages differed markedly from the streambed communities in both composition and functional organisation, with more collector-gatherers and predators in the interstitial zone and more filterers and scrapers in the natural riverbed. In Apennine lotic systems, the interstitial zone is an important habitat for stream macrobenthos, although it may not be used by all species.     

Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences

Invasion of two PNA strands to double-stranded DNA is one of the most promising methods to recognize a predetermined site in double-stranded DNA (PNA = peptide nucleic acid). In order to facilitate this 'double-duplex invasion', a new type of PNA was prepared by using chiral PNA monomers in which a nucleobase was bound to the alpha-nitrogen of N-(2-aminoethyl)-d-lysine. These positively charged monomer units, introduced to defined positions in Nielsen's PNAs (poly[N-(2-aminoethyl)glycine] derivatives), promoted the invasion without impairing mismatch-recognizing activity. When pseudo-complementary nucleobases 2,6-diaminopurine and 2-thiouracil were bound to N-(2-aminoethyl)-d-lysine, the invasion successfully occurred even at highly G-C-rich regions [e.g. (G/C)7(A/T)3 and (G/C)8(A/T)2] which were otherwise hardly targeted. Thus, the scope of sequences available as the target site has been greatly expanded. In contrast with the promotion by the chiral PNA monomers derived from N-(2-aminoethyl)-d-lysine, their l-isomers hardly invaded, showing crucial importance of the d-chirality. The promotion of double-duplex invasion by the chiral (d) PNA monomer units was ascribed to both destabilization of PNA/PNA duplex and stabilization of PNA/DNA duplexes.     

Activity and Diversity of Sulfate-Reducing Bacteria in a Petroleum Hydrocarbon-Contaminated Aquifer

Microbial sulfate reduction is an important metabolic activity in petroleum hydrocarbon (PHC)-contaminated aquifers. We quantified carbon source-enhanced microbial SO₄²⁻ reduction in a PHC-contaminated aquifer by using single-well push-pull tests and related the consumption of sulfate and added carbon sources to the presence of certain genera of sulfate-reducing bacteria (SRB). We also used molecular methods to assess suspended SRB diversity. In four consecutive tests, we injected anoxic test solutions (1,000 liters) containing bromide as a conservative tracer, sulfate, and either propionate, butyrate, lactate, or acetate as reactants into an existing monitoring well. After an initial incubation period, 1,000 liters of test solution-groundwater mixture was extracted from the same well. Average total test duration was 71 h. We measured concentrations of bromide, sulfate, and carbon sources in native groundwater as well as in injection and extraction phase samples and characterized the SRB population by using fluorescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE). Enhanced sulfate reduction concomitant with carbon source degradation was observed in all tests. Computed first-order rate coefficients ranged from 0.19 to 0.32 day⁻¹ for sulfate reduction and from 0.13 to 0.60 day⁻¹ for carbon source degradation. Sulfur isotope fractionation in unconsumed sulfate indicated that sulfate reduction was microbially mediated. Enhancement of sulfate reduction due to carbon source additions in all tests and variability of rate coefficients suggested the presence of specific SRB genera and a high diversity of SRB. We confirmed this by using FISH and DGGE. A large fraction of suspended bacteria hybridized with SRB-targeting probes SRB385 plus SRB385-Db (11 to 24% of total cells). FISH results showed that the activity of these bacteria was enhanced by addition of sulfate and carbon sources during push-pull tests. However, DGGE profiles indicated that the bacterial community structure of the dominant species did not change during the tests. Thus, the combination of push-pull tests with molecular methods provided valuable insights into microbial processes, activities, and diversity in the sulfate-reducing zone of a PHC-contaminated aquifer.     

First data on the nuclear DNA content (Feulgen-positive material) of Perodicticus potto

The nuclear DNA content (Feulgen-positive material) of Perodicticus potto, measured on lymphocytes from six animals of the subspecies edwarsi (Gabon) and potto (Dahomey and Liberia) is quite homogeneous around a mean value of 6·87 ± 0·15 pg. A difference of 1·5% has been found between sexes in each subspecies; the possible relation of this fact to the characteristics of the karyotype is discussed.     

Intrinsic competition between two European egg parasitoids of the brown marmorated stink bug

Following the accidental introduction and spread of the invasive polyphagous agricultural pest Halyomorpha halys (Stål) (Hemiptera: Pentatomidae), the two European egg parasitoids Anastatus bifasciatus (Geoffroy) (Hymenoptera: Eupelmidae) and Ooencyrtus telenomicida (Vassiliev) (Hymenoptera: Encyrtidae) have been investigated for inundative biological control. Since the competititve outcome between the two generalist parasitoids is difficult to predict, intrinsic competition was investigated with a time-course development study. Both species readily oviposited in H. halys eggs containing eggs and early instar larvae of the competitor, but oviposition decreased when eggs contained late instar larvae and pupae. Ooencyrtus telenomicida offspring emergence from multiparasitized eggs was significantly lower than that from rearing controls, independent of the order of parasitization. Anastatus bifasciatus offspring emergence was not influenced by the presence of O. telenomicida when it parasitized as the first species, but emergence was decreased after oviposition in eggs containing O. telenomicida larvae and pupae. There was no indication that O. telenomicida can act as a facultative hyperparasitoid of A. bifasciatus. These results suggest that A. bifasciatus is the superior intrinsic competitor and no or minor negative implications for A. bifasciatus are expected if released in combination with O. telenomicida.     

Soil organic carbon fractions in the Great Plains of the United States: an application of mid-infrared spectroscopy

Biogeochemistry - Spectroscopy is a powerful means of increasing the availability of soil data necessary for understanding carbon cycling in a changing world. Here, we develop a calibration...     

Meta-Fish-Lib: A generalised,dynamic DNA reference library pipeline for metabarcoding of fishes

The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready-to-use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish-12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish-12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta-Fish-Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib .