Optimizing a remotely sensed proxy for plankton biomass in Lake Kivu

Many regions of the world, including inland lakes, present with suboptimal conditions for the remotely sensed retrieval of optical signals, thus challenging the limits of available satellite data-processing tools, such as atmospheric correction models (ACM) and water constituent-retrieval (WCR) algorithms. Working in such regions, however, can improve our understanding of remote-sensing tools and their applicabil- ity in new contexts, in addition to potentially offering useful information about aquatic ecology. Here, we assess and compare 32 combinations of two ACMs, two WCRs, and three binary categories of data quality standards to optimize a remotely sensed proxy of plankton biomass in Lake Kivu. Each parameter set is compared against the available ground-truth match-ups using Spearman's right-tailed ρ. Focusing on the best sets from each ACM-WCR combination, their performances are discussed with regard to data distribution, sample size, spatial completeness, and seasonality. The results of this study may be of interest both for ecological studies on Lake Kivu and for epidemio- logical studies of disease, such as cholera, the dynamics of which has been associated with plankton biomass in other regions of the world.

Biomass and abundance of termites in three remnant areas of Atlantic Forest in northeastern Brazil

Termite biomass and abundance were estimated in three remnant areas of Atlantic Forest in northeastern Brazil: Reserva Biológica de Pedra Talhada-RBPT (Alagoas State), Parque Estadual Dois Irmãos-PEDI (Pernambuco State), and Área de Proteção Ambiental Mata do Buraquinho-APMB (Paraíba State). A quantitative sampling of the termite assemblages present on trunks and leaf litter, in nests, and in the soil was undertaken during the months of June and July (rainy season) and November and December (dry season) of 2000. Thirty seven species of termites were encountered and quantified in the three remnant forest areas. The termite biomass varied from 10.09 to 11.30 g (fresh weight)/m² and abundance varied from 4911 to 5663 individuals/m². The subfamily Nasutitermitinae was dominant in terms of the number of species, biomass, and abundance. The soil-feeders were the most abundant at the three sites, while wood-feeders had the largest biomass at least at the PEDI and APMB sites. Among the microhabitats quantified, termites were most frequently encountered in the soil, being most heavily concentrated at depths of 0-20 cm. Two species stood out in terms of their biomass and abundance: Embiratermes parvirostris Constantino, on the soil, and Nasutitermes corniger (Motschulsky), on decomposing trunks and in nests. Estimates of biomass and abundance suggest that termites play an important role in the decomposition of the plant necromass in remnant forest areas of the Atlantic Forest in northeastern Brazil.

Horizontal and vertical distributions of zooplanckton numbers and biomass off the coast of Peru

Estudio de las distribuciones horizontales y verticales del zooplancton a lo largo de una línea desde cerca de la costa hasta el borde de la plataforma.

Stable isotope and trace element stratigraphy across the Permian-Triassic transition: A redefinition of the boundary in the Velebit Mountain, Croatia

Stable isotopes of carbonates (delta(13)C(carb), delta(18)O(carb)), organic matter (delta(13)C(org), delta(15)N(org)) and major, trace and rare earth element (REE) compositions of marine carbonate rocks of Late Permian to Early Triassic age were used to establish the position of the Permian-Triassic boundary (PTB) at two continuous sections in the Velebit Mountain, Croatia. The chosen sections - Rizvanusa and Brezimenjaca - are composed of two lithostratigraphic units, the Upper Permian Transitional Dolomite and the overlying Sandy Dolomite. The contact between these units, characterized by the erosional features and sudden occurrence of ooids and siliciclastic grains, was previously considered as the chronostratigraphic PTB. The Sandy Dolomite is characterized by high content of non-carbonate material (up to similar to 30 wt.% insoluble residue), originated from erosion of the uplifted hinterland. A relatively rich assemblage of Permian fossils (including Geinitzina, Globivalvulina, Hemigordius, bioclasts of gastropods, ostracods and brachiopods) was found for the first time in Sandy Dolomite, 5 m above the lithologic boundary in the Rizvanusa section. A rather abrupt negative delta(13)C(carb) excursion in both sections appears in rocks showing no recognizable facies change within the Sandy Dolomite, -2 parts per thousand at Rizvanusa and -1.2 parts per thousand at Brezimenjaca, 11 m and 0.2 m above the lithologic contact, respectively. This level within the lower part of the Sandy Dolomite is proposed as the chemostratigraphic PTB. In the Rizvanusa section, the delta(13)C(org) values decline gradually from similar to-25 parts per thousand in the Upper Permian to similar to-29 parts per thousand in the Lower Triassic. The first negative delta(13)C(org) excursion occurs above the lithologic contact, within the uppermost Permian deposits, and appears to be related to the input of terrigenous material. The release of isotopically light microbial soil-biomass into the shallow-marine water may explain this sudden decrease of delta(13)C(org) values below the PTB. This would support the hypothesis that in the western Tethyan realm the land extinction, triggering a sudden drop of woody vegetation and related land erosion, preceded the marine extinction. The relatively low delta(15)N(org) values at the Permian-Triassic (P-Tr) transition level, close to approximate to 0 parts per thousand, and a secondary negative delta(13)C(org) excursion of -0.5 parts per thousand point to significant terrestrial input and primary contribution of cyanobacteria. The profiles of the concentrations of redox-sensitive elements (Ce, Mn, Fe, V), biogenic or biogenic-scavenged elements (P, Ba, Zn, V), Ce/Ce* values, and normalized trace elements, including Ba/Al, Ba/Fe, Ti/Al, Al/(Al + Fe + Mn) and Mn/Ti show clear excursions at the Transitional Dolomite-Sandy Dolomite lithologic boundary and the chemostratigraphic P-Tr boundary. The stratigraphic variations indicate a major regression phase marking the lithologic boundary, transgressive phases in the latest Permian and a gradual change into shallow/stagnant anoxic marine environment towards the P-Tr boundary level and during the earliest Triassic. (C) 2010 Elsevier B.V. All rights reserved.

Biosphere/lithosphere interface : microbially-mediated CaCO3 precipitation in hypersaline and freshwater environments

Abstract: Microbial mats very efficiently cycle elements, such as C, 0, N, S and H, which makes them key players of redox processes at the biosphere-lithosphere interface. They are characterized by high metabolic activities and high turnover rates (production and consumption) of biomass, which mainly consists of cell material and of extracellular organic matter (EOM). The EOM forms a matrix, embedding the microbial cells and fulfilling various functions within the microbial mat, including: mat attachment to surfaces; creation of micro-domains within the mat; physical stabilization under hy- drodynamic stress and the protection of the cells in multiple other stress conditions. EOM mainly consists of polysaccharides, amino acids, and a variety of chemical func-tional groups {e.g., -C00H, - SH -OH). These groups strongly bind cations such as Ca2+ and Mg2+ and thus exert a strong control on carbonate mineral formation within the microbial mat. A feedback mechanism between community metabolisms, their prod¬ucts, and the surrounding physicochemical microenvironment thus influences the de¬gree of carbonate saturation favoring either carbonate precipitation or dissolution. We investigated the driving forces and mechanisms of microbialite formation in the Sari ne River, FR, Switzerland, the hypersaline lake, Big Pond, Bahamas and in labo¬ratory experiments. The two fundamentally different natural systems allowed us to compare the geochemical conditions and microbial metabolisms, necessary for car¬bonate formation in microbial mats. Although carbonates are oversaturated in both environments, precipitation does not occur on physicochemical substrates (i.e. out¬side the microbial mats). In the Sarine a high crystal nucleation threshold exceeds the carbonate saturation, despite the high carbonate alkalinity in the water column. Cyanobacterial photosynthesis strongly locally enhances the carbonate alkalinity, whereas the EOM attract and immobilize calcium, which increases the saturation state and finally leads to carbonate precipitation within the EOM (in this case the cyanobacterial sheath) as nucleation template. In Big Pond, the presence of calcium- chelating anions (i.e. sulfate) and EOM, as well as the presence of magnesium, lowers the calcium activity in the water column and mat, and thus inhibits carbonate pre¬cipitation. Coupled with other heterotrophic metabolisms, sulfate reduction uses the EOM as carbon source, degrading it. The resulting EOM consumption creates alkalin¬ity, releases calcium and consumes sulfate in mat-micro domains, which leads to the formation of carbonate layers at the top of the microbial mat. Résumé: Interface biosphère/lithosphère: médiation microbienne de la précipitation de CaC03 dans des environnements en eaux douces et hypersalines Les tapis microbiens engendrent une circulation très efficace des éléments, tels que C, 0, N, S et H, ce qui en fait des acteurs clé pour les processus d'oxydoréduction à l'inter¬face biosphère-lithosphère. Ils sont caractérisés par des taux élevés d'activité méta¬bolique, ainsi que par la production et la consommation de biomasse, principalement constituée de cellules microbiennes et de matière organique extracellulaire (MOE). Dans un tapis microbien, les cellules microbiennes sont enveloppées par une matrice de MOE qui a différentes fonctions dont l'attachement du tapis aux surfaces, la créa¬tion de micro-domaines dans le tapis, la stabilisation physique en situation de stress hydrodynamique, et la protection des cellules dans de multiples autres conditions de stress. La MOE se compose principalement de polysaccharides, d'acides aminés, et d'une variété de groupes fonctionnels chimiques (par exemple, COOH, -SH et -OH). Ces groupes se lient fortement aux cations, tels que Ca2+ et Mg2+, et exercent ainsi un contrôle fort sur la formation de CaC03 dans le tapis microbien. Un mécanisme de rétroaction, entre les métabolismes de la communauté microbienne, leurs produits, et le microenvironnement physico-chimique, influence le degré de saturation de car¬bonate, favorisant soit leur précipitation, soit leur dissolution. Nous avons étudié le moteur et les mécanismes de minéralisation dans des tapis de la Sarine, FR, Suisse et du lac hypersalin, Big Pond, aux Bahamas, ainsi que durant des expériences en laboratoire. Les deux systèmes naturels, fondamentalement dif¬férents, nous ont permis de comparer les conditions géochimiques et les métabolis¬mes nécessaires à la formation des carbonates dans des tapis microbiens. Bien que les carbonates soient sursaturés dans les deux environnements, la précipitation ne se produit pas sur des substrats physico-chimiques (en dehors du tapis microbien). Dans la Sarine, malgré un taux d'alcalinité élevé, les valeurs de seuil pour la nucléa- tion de carbonates sont plus hautes que la saturation du carbonate. La photosynthèse cyanobactérienne augmente localement l'alcalinité, alors que la MOE attire et immo¬bilise le calcium, ce qui augmente l'état de saturation et conduit finalement à la pré¬cipitation des carbonates, en utilisant la MOE comme substrat de nucléation. À Big Pond, la présence de chélateurs de calcium, notamment les anions (p.ex. le sulfate) et la MOE, ainsi que la présence de magnésium, réduit l'activité du calcium et inhibe en conséquence la précipitation des carbonates. Couplée avec d'autres métabolismes hétérotrophes, la réduction des sulfates utilise la MOE comme source de carbone, en la dégradant. Cette consommation de MOE crée l'alcalinité, consomme des sulfates et libère du calcium dans des micro-domaines, conduisant à la formation de couches de carbonates dans le haut du tapis microbien.

Stocks assesment, biomass and fish production in two mediterranean basins (NE Spain)

In order to evaluate the success of the reintroduction of the Eurasian otter (Lutra lutra) in the Empordh wetlands (Parc Natural dels Aiguamolls de I'Empordhà), and the Muga and Fluvih basins, density of fish, biomass and production in the Muga and Fluvia Rivers have been estimated, since fishes represent the principal prey in the otter diet. 12 study sites were selected in order to survey the main flows in both basins. Electrofishing surveys were conducted by blocking off the station with barrier nets, which was performed upon 3 successive catches. The density estimated presents a range of 1,136-1 25 ind .ha' in the Muga basin, 4,49-163 ind.ha' in the Fluvih basin and 3,76-52,2 ind.ha' in the Empordh wetlands. Estimated biomass ranges are 0,616-277,6 g.m2, 8,79-351,2 g.m2, and 5,7-108 g.m-2 respectively. These density anfi biomass ranges are similar to other results obtained from rivers inhabited by the Eurasian otter in NE Spain

Biomass estimation of Triplectides egleri Sattler (Trichoptera, Leptoceridae) in a stream at Ducke Reserve, Central Amazonia

ABSTRACT Biomass is a fundamental measure for understanding the structure and functioning (e.g. fluxes of energy and nutrients in the food chain) of aquatic ecosystems. We aim to provide predictive models to estimate the biomass of Triplectides egleri Sattler, 1963, in a stream in Central Amazonia, based on body and case dimensions. We used body length, head-capsule width, interocular distance and case length and width to derive biomass estimations. Linear, exponential and power regression models were used to assess the relationship between biomass and body or case dimensions. All regression models used in the biomass estimation of T. egleri were significant. The best fit between biomass and body or case dimensions was obtained using the power model, followed by the exponential and linear models. Body length provided the best estimate of biomass. However, the dimensions of sclerotized structures (interocular distance and head-capsule width) also provided good biomass predictions, and may be useful in estimating biomass of preserved and/or damaged material. Case width was the dimension of the case that provided the best estimate of biomass. Despite the low relation, case width may be useful in studies that require low stress on individuals.

Assessment of microbial community structure changes by amplified ribosomal DNA restriction analysis (ARDRA)

Amplified ribosomal DNA restriction analysis (ARDRA) is a simple method based on restriction endonuclease digestion of the amplified bacterial 16S rDNA. In this study we have evaluated the suitability of this method to detect differences in activated sludge bacterial communities fed on domestic or industrial wastewater, and subject to different operational conditions. The ability of ARDRA to detect these differences has been tested in modified Ludzack-Ettinger (MLE) configurations. Samples from three activated sludge wastewater treatment plants (WWTPs) with the MLE configuration were collected for both oxic and anoxic reactors, and ARDRA patterns using double enzyme digestions AluI+MspI were obtained. A matrix of Dice similarity coefficients was calculated and used to compare these restriction patterns. Differences in the community structure due to influent characteristics and temperature could be observed, but not between the oxic and anoxic reactors of each of the three MLE configurations. Other possible applications of ARDRA for detecting and monitoring changes in activated sludge systems are also discussed

Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, a revolution in clinical microbial identification.

Until recently, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) techniques for the identification of microorganisms remained confined to research laboratories. In the last 2 years, the availability of relatively simple to use MALDI-TOF MS devices, which can be utilized in clinical microbiology laboratories, has changed the laboratory workflows for the identification of pathogens. Recently, the first prospective studies regarding the performance in routine bacterial identification showed that MALDI-TOF MS is a fast, reliable and cost-effective technique that has the potential to replace and/or complement conventional phenotypic identification for most bacterial strains isolated in clinical microbiology laboratories. For routine bacterial isolates, correct identification by MALDI-TOF MS at the species level was obtained in 84.1-93.6% of instances. In one of these studies, a protein extraction step clearly improved the overall valid identification yield, from 70.3% to 93.2%. This review focuses on the current state of use of MALDI-TOF MS for the identification of routine bacterial isolates and on the main difficulties that may lead to erroneous or doubtful identifications.

Changes in understorey biomass and species composition after water level drawdown on pine mires in southern Finland

Tiivistelmä: Vedenpinnan alenemisen vaikutus sararämeen pintakasvillisuuden biomassaan ja lajistoon

Surface and subsurface decomposition of a desiccated grass pasture biomass related to erosion and its prediction with RUSLE

Erosion is deleterious because it reduces the soil's productivity capacity for growing crops and causes sedimentation and water pollution problems. Surface and buried crop residue, as well as live and dead plant roots, play an important role in erosion control. An efficient way to assess the effectiveness of such materials in erosion reduction is by means of decomposition constants as used within the Revised Universal Soil Loss Equation - RUSLE's prior-land-use subfactor - PLU. This was investigated using simulated rainfall on a 0.12 m m-1 slope, sandy loam Paleudult soil, at the Agriculture Experimental Station of the Federal University of Rio Grande do Sul, in Eldorado do Sul, State of Rio Grande do Sul, Brazil. The study area had been covered by native grass pasture for about fifteen years. By the middle of March 1996, the sod was mechanically mowed and the crop residue removed from the field. Late in April 1996, the sod was chemically desiccated with herbicide and, about one month later, the following treatments were established and evaluated for sod biomass decomposition and soil erosion, from June 1996 to May 1998, on duplicated 3.5 x 11.0 m erosion plots: (a) and (b) soil without tillage, with surface residue and dead roots; (c) soil without tillage, with dead roots only; (d) soil tilled conventionally every two-and-half months, with dead roots plus incorporated residue; and (e) soil tilled conventionally every six months, with dead roots plus incorporated residue. Simulated rainfall was applied with a rotating-boom rainfall simulator, at an intensity of 63.5 mm h-1 for 90 min, eight to nine times during the experimental period (about every two-and-half months). Surface and subsurface sod biomass amounts were measured before each rainfall test along with the erosion measurements of runoff rate, sediment concentration in runoff, soil loss rate, and total soil loss. Non-linear regression analysis was performed using an exponential and a power model. Surface sod biomass decomposition was better depicted by the exponential model, while subsurface sod biomass was by the power model. Subsurface sod biomass decomposed faster and more than surface sod biomass, with dead roots in untilled soil without residue on the surface decomposing more than dead roots in untilled soil with surface residue. Tillage type and frequency did not appreciably influence subsurface sod biomass decomposition. Soil loss rates increased greatly with both surface sod biomass decomposition and decomposition of subsurface sod biomass in the conventionally tilled soil, but they were minimally affected by subsurface sod biomass decomposition in the untilled soil. Runoff rates were little affected by the studied treatments. Dead roots plus incorporated residues were effective in reducing erosion in the conventionally tilled soil, while consolidation of the soil surface was important in no-till. The residual effect of the turned soil on erosion diminished gradually with time and ceased after two years.

Backseat drivers: the hidden influence of microbial viruses on disease.

Because viral replication depends on the vigour of its host, many viruses have evolved incentives of fitness to pay their keep. When the viral host is a human pathogen, these fitness factors can surface as virulence: creating a Russian doll of pathogenesis where pathogens within pathogens complicate the disease process. Microbial viruses can even be independently immunogenic, as we recently reported for leishmania-virus. Thus, the incidence of this 'hyperpathogenism' is becoming an important clinical consideration and by appreciating the microbial-virus as a backseat driver of human disease, we could exploit its presence as a diagnostic biomarker and molecular target for therapeutic intervention. Here we discuss the prevalence of clinically relevant hyperpathogenism as well as the environmental sanctuaries that breed it.