Sequentially aerated membrane biofilm reactors for autotrophic nitrogen removal: microbial community composition and dynamics

Membrane-aerated biofilm reactors performing autotrophic nitrogen removal can be successfully applied to treat concentrated nitrogen streams. However, their process performance is seriously hampered by the growth of nitrite oxidizing bacteria (NOB). In this work we document how sequential aeration can bring the rapid and long-term suppression of NOB and the onset of the activity of anaerobic ammonium oxidizing bacteria (AnAOB). Real-time quantitative polymerase chain reaction analyses confirmed that such shift in performance was mirrored by a change in population densities, with a very drastic reduction of the NOB Nitrospira and Nitrobacter and a 10-fold increase in AnAOB numbers. The study of biofilm sections with relevant 16S rRNA fluorescent probes revealed strongly stratified biofilm structures fostering aerobic ammonium oxidizing bacteria (AOB) in biofilm areas close to the membrane surface (rich in oxygen) and AnAOB in regions neighbouring the liquid phase. Both communities were separated by a transition region potentially populated by denitrifying heterotrophic bacteria. AOB and AnAOB bacterial groups were more abundant and diverse than NOB, and dominated by the r-strategists Nitrosomonas europaea and Ca. Brocadia anammoxidans, respectively. Taken together, the present work presents tools to better engineer, monitor and control the microbial communities that support robust, sustainable and efficient nitrogen removal

Accurate and early diagnosis of orthopedic device-related infection by microbial heat production and sonication.

Proper and rapid diagnosis of orthopedic device-related infection is important for successful treatment. Sonication has been shown to improve the diagnostic performance. We hypothesized that the combination of sonication with a novel method called microcalorimetry will further improve and accelerate the diagnosis of implant infection. We prospectively included 39 consecutive patients (mean age 59 years, 62% males) at our institution from whom 29 orthopedic prostheses and 10 osteosynthesis material were explanted. The explanted device was sonicated. The resulting sonication fluid was analyzed using microcalorimetry. Using standardized criteria to define orthopedic device-related infection, 12 cases (31%) were defined as infected. In all, positive periprosthetic tissue cultures were found. The sensitivity and specificity of microcalorimetry of sonication fluid were 100% and 97%, respectively. Mean time to detection, defined as time to reach a rising heat flow signal of 20 µW measured after equilibiration needed to get accurate measurement, was 10.9 h. In summary, microcalorimetry of sonication fluid is a reliable and a fast method in detecting the presence of microorganisms in orthopedic device-related infection. © 2013 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 31:1700-1703, 2013.

Development, structure and distribution of colleters in Mandevilla illustris and M. velutina (Apocynaceae)

Colleters of Mandevilla illustris and M. velutina are present on the cotyledons, shoot apices, mature leaves and on the nodal region, where they are interpetiolar and intrapetiolar. In M. velutina there are two colleters on the adaxial basal part of the leaf blade, and in M. illustris, this number varies. The differentiation of the colleters occurs in the early stages of leaf development. When colleters are mature, they consist of a long head on a short stalk. The central core of the colleter is made up of parenchymatous cells that may exhibit phenolic compounds and is surrounded by radially elongated epithelial cells. The foliar and intrapetiolar colleters can exhibit vascularization. The colleters produce a translucient sticky substance that reacts positively to polysaccharides and, before senescence, they produce lipophilic substances. The Mandevilla colleters data can give support to the taxonomy and phylogeny of the Apocynaceae.

Taxonomy and distribution of the green algal genus Halimeda (Bryopsidales, Chlorophyta) in Brazil

Halimeda is a genus of calcified coenocytic green algae with a well known ecological importance in some tropical areas. Bleached calcified segments of Halimeda may accumulate in large deposits of economic potential as is the case in the northeastern coast of Brazil. In a survey of the genus in Brazil based on recent collections and examination of abundant material deposited on Brazilian herbaria we identified seven species: Halimeda cuneata Hering, H. discoidea Decaisne, H. gracilis Harvey ex J. Agardh, H. incrassata (Ellis) Lamouroux, H. opuntia (Linnaeus) Lamouroux, H. simulans Howe and H. tuna (Ellis & Solander) Lamouroux. These species are described in detail, with emphasis on diagnostic characters. Our study has shown that the shape and size of the utricula in surface view, under scanning electron microscopy, can be utilized to discriminate some species. Fertile specimens of Halimeda cuneata and H. discoidea are reported for the first time in the region. Data on vertical and geographical distribution are presented for each species and the southern limit of the genus in the western Atlantic was extended.

Taxonomy and Species Richness of Amazonian Pimplinae and Rhyssinae (hymenoptera: ichneumonidae)

The Amazonian region, the biggest rain forest of our planet, is known for its extraordinary biodiversity. Most of this diversity is still unexplored and new species of different taxa are regularly found there. In this region, as in most areas of the world, insects are some of the most abundant organisms. Therefore, studying this group is important to promote the conservation of these highly biodiverse ecosystems of the planet. Among insects, parasitoid wasps are especially interesting because they have potential for use as biodiversity indicators and biological control agents in agriculture and forestry. The parasitoid wasp family Ichneumonidae is one of the most species rich groups among the kingdom Animalia. This group is still poorly known in many areas of the world; the Amazonian region is a clear example of this situation. Ichneumonids have been thought to be species poor in Amazonia and other tropical areas. However, recent studies are suggesting that parasitoid wasps may be quite abundant in Amazonia and possibly in most tropical areas of the world. The aim of my doctoral thesis is to study the species richness and taxonomy of two of the best known ichneumonid subfamilies in the Neotropical region, Pimplinae and Rhyssinae. To do this I conducted two extensive sampling programs in the Peruvian Amazonia. I examined also a large number of Neotropical ichneumonids deposited to different natural history museums. According to the results of my thesis, the species richness of these parasitoids in the Amazonian region is considerably higher than previously reported. In my research, I firstly further develop the taxonomy of these parasitoids by describing many new species and reporting several new faunistic records (I, II, III). In this first part I focus on two genera (Xanthopimpla and Epirhyssa) which were thought to be rather species poor. My thesis demonstrates that these groups are actually rather species rich in the Amazonian region. Secondly, I concentrate on the species richness of these parasitoids in a global comparison showing that the Neotropical region and especially the Peruvian Amazonia is one of the most species rich areas of Pimpliformes ichneumonids (V). Furthermore, I demonstrate that with the data available to date no clear latitudinal gradient in species richness is visible. Thirdly, increasing the macroecological knowledge of these parasitoids I show that some previously unreported ichneumonid subfamilies are present in the Amazonian region (IV). These new insights and the results of the global comparison of ichneumonid inventories suggest that the previous belief of low diversity in the tropics is most likely related to a lack of sampling effort in the region. Overall, my research increases the knowledge of Neotropical ichneumonids highlighting the importance of Peruvian Amazonia as one of the diversity hotspots of parasitoid wasps.

Effect of starter culture and inulin addition on microbial viability, texture, and chemical characteristics of whole or skim milk Kefir

The effect of inulin addition and starters (Kefir grains or commercial starter culture) on the microbial viability, texture, and chemical characteristics of Kefir beverages prepared with whole or skim milk was evaluated during refrigerated storage. The type of starter did not influence microbial viability during the storage of the beverages, but the chemical and textural changes (decreases in pH, lactose concentration, and inulin and increased acidity, firmness, and syneresis) were more pronounced in the formulations fermented with grains than those fermented with the starter culture. The addition of inulin did not influence acidity or viability of lactic acid bacteria, but in general, its effect on the survival of acetic acid bacteria, Lactococcus and yeasts, firmness, and syneresis depended on the type of milk and starter culture used. Generally, the yeast, acetic acid bacteria, and Leuconostoc counts increased or remained unchanged, while the total population of lactic acid bacteria and Lactococcus were either reduced by 1 to 2 logs or remained unchanged during storage.

Investigating Microbial Trace-fossils and Abiotic Alteration in Hydrovolcanic Tuffs of the Fort Rock Volcanic Field, Oregon

Microbial ichnofossils in volcanic rocks provide a significant record of subsurface microbes and potentially extraterrestrial biosignatures. Here, the textures, mineralogy, and geochemistry of two continental basaltic hydrovolcanic deposits - Reed Rocks and Black Hills - in the Fort Rock Volcanic Field (FRVF) are investigated. Methods include petrographic microscopy, micro and powder X-ray diffraction, SEM/BSE/EDF imaging, energy dispersive spectroscopy, stable isotopes, and X-ray fluorescence. Petrographic analysis revealed granular and tubular textures with biogenic morphologies that include terminal enlargements, septate divisions, branching forms, spiral filaments, and ovoid bodies resembling endolithic microborings described in ocean basalts. They display evidence of behaviour and a geologic context expressing their relative age and syngenicity. Differences in abiotic alteration and the abundance/morphotype assemblage of putative microborings between the sites indicate that water/rock ratio, fluid composition and flux, temperature and secondary phase formation are influences on microboring formation. This study is the first report of reputed endolithic microborings in basalts erupted in a continental lacustrine setting.

INDIAN AND ANTARCTIC BRYOZOANS - TAXONOMY AND OBSERVATIONS ON TOXICOLOGY

This thesis embodies findings on a taxonomical investigation of a group of lower marine invertebrates belonging to the category coelomata. Bryozoans are well known both in fossil and recent taxonomical history. They comprise of about 5,000 living and 16000 fossil species. Bryozoans are well known for their taxonomic abundance and structural diversity,representing the various ecological niches ranging from the intertidal to the abyssal benthic. At a time when global marine biological diversity has become a concern of not only to the scientists but also to the policy makers,an understanding of species diversity and abundance are cardinal aspects of biological studies. Geological time scales which is known that by Pre-Cambrian, marine invertebrate diversity reach the maximum and this diversity has become more comprehensive as time advanced. Taxonomists a vanishing species of scientists have become more concerned in discerning patterns of species diversity. The basic tool for this is identification fo animals. with this idea in mind a detailed study of taxonomy of bryozoan was undertaken . The major part of this thesis is devoted to describe various species of bryozoans with detailed description and ecotypical variations.The pattern of distribution and abundance which are important aspects of animal groups have also been documented. Possible effects of heavy metal contamination on the tolerance and growth of bryozoans, a few species of which have been eliminated from the chronically polluted areas of Cochin backwaters have also been documented.

Systematics, Bionomics and Seed Production of Macrobrachium spp. of the Vembanad Lake

School of Industrial Fisheries, Cochin University of Science and Technology

Studies on the systematics, biology and fishery of rainbow sardines, dussumieria spp., from Indian waters

Rainbow sardines of the genus belonging to the family Dueenaieriidae. are small pelagic fishes forming a fairly good, though not abundant. seasonal fishery all along the coasts of India inhabiting the coastal waters. There have been some earlier reports on such individual aspects as their systematic, distribution, abundance. Ostecology and a few biological factors but no attempt has been made towards a comprehensive study on this group. Two species of rainbow sardines are known to occur in the Indian seas and while a knowledge about their biology would be useful from the fishery point of view. it was also thought a study of their systematic position, especially regarding the identity or the two species which had raised doubts among earlier workers would lead to a better understanding or the group as a whole. This thesis is mainly based on studies during the period from April 1969 to march 1971 with a continued investigation of fishhery aspects till December 1975. from the Gulf of manar: and the Palk Bay around mandapam area. on the south-east coast of India. Thus the work deals with the systemtics, biology and fishery of rainbow sardines of Indian seas.

A new isoform of anti-lipopolysaccharide factor identified from the blue swimmer crab, Portunus pelagicus: Molecular characteristics and phylogeny

Anti-lipopolysaccharide factors are small proteins that bind and neutralize lipopolysaccharide and exhibit potent antimicrobial activities. This study presents the molecular characterization and phylogenetic analysis of the first ALF isoform (Pp-ALF1; JQ745295) identified from the hemocytes of Portunus pelagicus. The full length cDNA of Pp-ALF1 consisted of 880 base pairs encoding 293 amino acids with an ORF of 123 amino acids and contains a putative signal peptide of 24 amino acids. Pp-ALF1 possessed a predicted molecular weight (MW) of 13.86 kDa and theoretical isoelectric point (pI) of 8.49. Two highly conserved cysteine residues and putative LPS binding domain were observed in Pp-ALF1. Peptide model of Pp-ALF1 consisted of two α-helices crowded against a four-strand β-sheet. Comparison of amino acid sequences and neighbor joining tree showed that Pp-ALF1 has a maximum similarity (46%) to ALF present in Portunus trituberculatus followed by 39% similarity to ALF of Eriocheir sinensis and 38% similarity to ALFs of Scylla paramamosain and Scylla serrata. Pp-ALF1 is found to be a new isoform of ALF family and its characteristic similarity with other known ALFs signifies its role in protection against invading pathogens.

A Novel Isoform of the Hepatic Antimicrobial Peptide, Hepcidin (Hepc-CB1), from a Deep-Sea Fish, the Spinyjaw Greeneye Chlorophthalmus bicornis (Norman, 1939): Molecular Characterisation and Phylogeny

Hepcidin is cysteine-rich short peptide of innate immune system of fishes, equipped to perform prevention and proliferation of invading pathogens like bacteria and viruses by limiting iron availability and activating intracellular cascades. Hepcidins are diverse in teleost fishes, due to the varied aquatic environments including exposure to pathogens, oxygenation and iron concentration. In the present study, we report a 87-amino acid (aa) preprohepcidin (Hepc-CB1) with a signal peptide of 24 aa, a prodomain of 39 aa and a bioactive mature peptide of 24 aa from the gill mRNA transcripts of the deep-sea fish spinyjaw greeneye, Chlorophthalmus bicornis. Molecular characterisation and phylogenetic analysis categorised the peptide to HAMP2-like group with a mature peptide of 2.53 kDa; a net positive charge (?3) and capacity to form b-hairpin-like structure configured by 8 conserved cysteines. The present work provides new insight into the mass gene duplication events and adaptive evolution of hepcidin isoforms with respect to environmental influences and positive Darwinian selection. This work reports a novel hepcidin isoform under the group HAMP2 from a nonacanthopterygian deep-sea fish, C. bicornis

Effects of grassland conversion and tillage intensities on soil microbial biomass, residues and community structure

Agricultural intensification has a strong impact on level of soil organic matter (SOM), microbial biomass stocks and microbial community structure in agro-ecosystems. The size of the microbial necromass C pool could be about 40 times that of the living microbial biomass C pool in soils. Due to the specificity, amino sugar analysis gives more important information on the relative contribution of fungal and bacterial residues to C sequestration potential of soils. Meanwhile, the relationship between microbial biomass and microbial necromass in soil and its ecological significance on SOM are not fully understood and likely to be very complex in grassland soils. This thesis focuses on the effects of tillage, grassland conversion intensities and fertilisation on microbial biomass, residues and community structure. The combined analyses of microbial biomass and residue formation of both fungi and bacteria provided a unique opportunity to study the effect of tillage, grassland conversion and fertilisation on soil microbial dynamics. In top soil at 0-30 cm layer, a reduction in tillage intensity by the GRT and NT treatments increased the accumulation of saprotrophic fungi in comparison with the MBT treatment. In contrast, the GRT and NT treatments promoted AMF at the expense of saprotrophic fungi in the bottom soil layer at 30-40 cm depth. The negative relationship between the ergosterol to microbial biomass C ratio and the fungal C to bacterial C ratio points to the importance of the relationship between saprotrophic fungi and biotrophic AMF for tillage-induced changes in microbial turnover of SOC. One-season cultivation of winter wheat with two tillage events led to a significant loss in SOC and microbial biomass C stocks at 0-40 cm depth in comparison with the permanent grassland, even 5 years after the tillage event. However, the tillage induced loss in microbial biomass C was roughly 40% less in the long-term than in the short-term of the current experiment, indicating a recovery process during grassland restoration. In general, mould board tillage and grassland conversion to maize monoculture promoted saprotrophic fungi at the expense of biotrophic AMF and bacteria compared to undisturbed grassland soils. Slurry application promoted bacterial residues as indicated by the decreases in both, the ergosterol to microbial biomass C ratio and the fungal C to bacterial C ratio. In addition, the lost microbial functional diversity due to tillage and maize monoculture was restored by slurry application both in arable and grassland soils. I conclude that the microbial biomass C/S ratio can be used as an additional indicator for a shift in microbial community. The strong relationships between microbial biomass and necromass indices points to the importance of saprotrophic fungi and biotrophic AMF for agricultural management induced effects on microbial turnover and ecosystem C storage. Quantitative information on exact biomass estimates of these two important fungal groups in soil is inevitably necessary to understand their different roles in SOM dynamics.