Ecosystem functioning, or the role which organisms play in an ecosystem, is becoming increasingly important in marine ecological and conservation. To facilitate such studies an international team of scientists lead by S. Faulwetter from the Hellenic Centre for Marine Research (HMRC) present the Polytraitsdatabase that aims to provide re-usable, and accessible data on marine bristle worms. The paper describing the new database was published in the innovative Biodiversity Data Journal, a pioneer in the publication of integrated biological data.

Benthic organisms participate in a number of biological processes in world water basins. Their functional diversity is an important community property demonstrating the role organisms have in the ecosystem and helping to understand how the community reacts to environmental changes. Polychaetes, or bristle worms, are marine worms famous for their peculiar shapes and often vivid coloration. More than 10,000 species are described in the class worldwide, most of which living in the shelf zone of the seas and oceans, burrowing in the sediment or swimming among the plankton.

At present, the Polytraits database contains almost 20,000 records on morphological, behavioural and reproductive characteristics of more than 1,000 species, all referenced by literature sources. All data on these engaging organisms can be freely accessed through the project website in different ways and formats, both human-readable and machine-readable. The new database presents a rich and easy to use collection, which cover morphological, reproductive and behavioural characteristics of polychaetes, as well as information on environmental preferences in an attempt to facilitate ecological research and conservation studies.

The researchers also provide a leading-edge approach to accessing, integrating and re-using the data. Through programming interfaces, the life-cycle information is automatically integrated into the Polychaetes Scratchpads, together with other data on polychaetes. Scratchpads are easy to use, adaptable, and provide powerful tools for managing biodiversity data. This taxon-centric virtual research environment allows browsing the taxonomic classification and retrieving various kinds of relevant information for each taxon, among which are also the collected biological traits.

Furthermore, the data are also accessible through Encyclopedia of Life's TraitBank which currently features over 3 million records related to more than 250 attributes for 272,720 taxa, including the Polytraits data. TraitBank serves as a provider for aggregated species trait data. All data uploaded there are archived and integrated with trait information from other sources to address issues of standardization of scientific data. This is the first complex database for marine organisms to be published in such an innovative way and demonstrates yet another example of collaboration between the data publisher Pensoft and Encyclopedia of Life.

Full article available at: http://dx.doi.org/10.1186/1471-2105-12-S15-S1 

The emerging science of gene drives has the potential to address environmental and public health challenges, but gene-drive modified organisms are not ready to be released into the environment and require more research in laboratories and highly controlled field trials, says a new report from the National Academies of Sciences, Engineering, and Medicine.

Peter Lasch
Dec 1, 2020; 19:2125-2138
Technological Innovation and Resources

Over the past decade, modern methods of MS (MS) have emerged that allow reliable, fast and cost-effective identification of pathogenic microorganisms. Although MALDI-TOF MS has already revolutionized the way microorganisms are identified, recent years have witnessed also substantial progress in the development of liquid chromatography (LC)-MS based proteomics for microbiological applications. For example, LC-tandem MS (LC-MS²) has been proposed for microbial characterization by means of multiple discriminative peptides that enable identification at the species, or sometimes at the strain level. However, such investigations can be laborious and time-consuming, especially if the experimental LC-MS² data are tested against sequence databases covering a broad panel of different microbiological taxa. In this proof of concept study, we present an alternative bottom-up proteomics method for microbial identification. The proposed approach involves efficient extraction of proteins from cultivated microbial cells, digestion by trypsin and LC–MS measurements. Peptide masses are then extracted from MS¹ data and systematically tested against an in silico library of all possible peptide mass data compiled in-house. The library has been computed from the UniProt Knowledgebase covering Swiss-Prot and TrEMBL databases and comprises more than 12,000 strain-specific in silico profiles, each containing tens of thousands of peptide mass entries. Identification analysis involves computation of score values derived from correlation coefficients between experimental and strain-specific in silico peptide mass profiles and compilation of score ranking lists. The taxonomic positions of the microbial samples are then determined by using the best-matching database entries. The suggested method is computationally efficient – less than 2 mins per sample - and has been successfully tested by a test set of 39 LC-MS¹ peak lists obtained from 19 different microbial pathogens. The proposed method is rapid, simple and automatable and we foresee wide application potential for future microbiological applications.

DNA analysis suggests Pando, a quaking aspen in Utah with thousands of stems connected by their roots, is between 16,000 and 81,000 years old

DNA analysis suggests Pando, a quaking aspen in Utah with thousands of stems connected by their roots, is between 16,000 and 81,000 years old

DNA analysis suggests Pando, a quaking aspen in Utah with thousands of stems connected by their roots, is between 16,000 and 81,000 years old

The conference will cover developments and the state-of-the art of environmental microbiology, as it is applied for biotechnological purposes, and the role of genetic engineering of micro-organisms intended for use in the environment, now and in the near future.

Micro-organisms play a fundamental role in the environment. Yet their role is the result of complex biogeochemical processes by consortia of micro-organisms and the function of individual species is not clear in many cases. This publication provides an overview of the current situation and relevant developments in environmental microbiology.

The emerging science of gene drives has the potential to address environmental and public health challenges, but gene-drive modified organisms are not ready to be released into the environment and require more research in laboratories and highly controlled field trials, says a new report from the National Academies of Sciences, Engineering, and Medicine.

Researchers have discovered high levels of plastic particles and fibres, as well as black carbon (BC), which is formed by the incomplete burning of fossil fuels, in the waters of the Jade Bay, an inshore basin off the coast of Germany in the Southern North Sea. The concentration of suspended particles are of concern because they have the potential to be ingested by fish and other marine life, and enter the food chain.

Converting grassland to arable land can reduce the diversity of nematodes, predatory mites, earthworms and enchytraeid worms in the soil, according to a study by Dutch researchers. However, they found that restoring arable land to grassland did not fully restore the diversity of these four groups during the course of the four-year study.

Converting grassland to arable land can reduce the diversity of nematodes, predatory mites, earthworms and enchytraeid worms in the soil, according to a study by Dutch researchers. However, they found that restoring arable land to grassland did not fully restore the diversity of these four groups during the course of the four-year study.

Almost a quarter of the world’s non-polar land surface experiences light pollution, and there is concern that this adversely affects illuminated ecosystems. Currently there is a global move from yellow sodium lighting to white LED lighting, which emits different wavelengths of light. A recent study found that LED artificial light at night (ALAN) reduced the biomass of periphyton by 62% in a freshwater drainage ditch in Westhavelland Nature Park, Brandenburg, Germany.

Recent research has found that silver nanoparticles in sewage sludge, which is used on agricultural land as a fertiliser, can be toxic to soil microorganisms. The researchers calculated that a maximum of 30mg of silver nanoparticles per kilogram of sludge can be applied to land before harm occurs, based on typical application rates in Germany of five tons per hectare of farmland every three years.

Nanotechnology is a key enabling technology predicted to have many societal benefits, but there are also concerns about its risks to the environment. This study reviewed the effects of nanoparticles on soil microorganisms, showing that toxicity depends on the type of particle. The researchers make recommendations for improving environmental risk assessment, including performing experiments in soil and over longer time periods.

Silver nanoparticles present in the effluent from waste-water treatment plants could have toxic effects on aquatic organisms, new research suggests. The lab-based study tested the effects of nanoparticle-containing effluent on several crustacean and algae species. The researchers observed that epibenthic crustaceans (those living in or on sediments at the bottom of water bodies) were the most sensitive; notably, a 20–45% higher death rate was observed compared with those exposed to nanoparticle-free effluent.

AR contents showing tidal flat organisms popular in Muan Ecological Tidal Flat Science Museum

Methods of separating renewable materials, such as lipids, from microorganisms, such as oleaginous yeasts, may include conditioning cell walls of the microorganisms to form, open or enlarge pores, and removing at least a portion of the renewable material through the pores. These methods may result in delipidated microorganisms with cell walls that are substantially intact and with mesopores. These delipidated microorganisms may be used to produce biofuels.

To provide a method which exerts excellent controlling effects on noxious organisms in a field of soybean, corn or cotton. A method for controlling noxious organisms in a field of soybean, corn or cotton, wherein at least one PPO inhibitor compound selected from the group consisting of flumioxazin, sulfentrazone, saflufenacil, oxyfluorfen, fomesafen-sodium, and a compound represented by formula (I): is applied to the field before, at or after sowing a soybean, corn or cotton seed treated with fludioxonil.

To provide a method which exerts excellent controlling effects on noxious organisms in a field of soybean, corn or cotton. A method for controlling noxious organisms in a field of soybean, corn or cotton, wherein at least one PPO inhibitor compound selected from the group consisting of flumioxazin, sulfentrazone, saflufenacil, oxyfluorfen, fomesafen-sodium, and a compound represented by formula (I): is applied to the field before, at or after sowing a soybean, corn or cotton seed treated with ethaboxam.

A method for enhancing the production of aquatic organisms under cultivation, including the steps of exposing the aquatic organisms to a submerged illumination source inside water of a rearing unit; and maintaining illumination in the rearing unit for a rearing period.

An elongate rectangular cultivation box having an open top, is configured so as to allow an outer tank, which serves as a cultivating water storage part, and an inner tank, which serves as a receptacle for bivalves (benthic organisms) S that are to be cultivated, to be both combined and separated. A gap that serves as a water supply opening and a gap that serves as a space in which sediments can accumulate on the bottom of the outer tank are defined when the inner tank is accommodated in the outer tank. Water passage holes are provided in the bottom of the shellfish receptacle (inner tank) and a mesh filter such as netting is stretched across the top face of the bottom. The cultivation boxes are arranged in a vertically stacked manner, with the front portions and rear portions thereof staggered so that cultivation water W that overflows over a front ledge of a shellfish receptacle flows downward into the supply water storage part of a lower cultivation box.

A method and processes to solubilize and transform phosphorus contents of rock phosphate (RP) into bio-organo-phosphate (BOP) fertilizer have been developed and integrated. The methods include collecting and sorting of organic wastes; blending with RP; subjecting the blend to biocomposting; collection, isolation, selection and growth optimization of consortia of efficient phosphorus solubilizing microorganisms (PSM) and novel plant growth regulating microorganisms (PGRM); where in PSM produce organic acids and other organic compounds using compost substrate at mesophillic stage, whereas the organic acids released during composting also act in synergism of PSM, thus forming a carbon rich acidic culture resulting in the solubilization of rock phosphate.

The present disclosure is directed toward a composition and method of treating and preventing infection of pathogenic microorganisms and endopyhtic microorganisms in a plant through the use of phosphite compositions.

A composition of matter comprising: a combination of a phytate and a plurality of microorganisms comprising a Trichoderma virens fungus, a Bacillus amyloliquefaciens bacterium, and one or a plurality of mycorrhizae fungi that is placed in the vicinity of a plant root in a manner that allows the microorganisms in the composition of matter to colonize said plant root; and a method for increasing plant yield comprising: placing a combination of a phytate and a plurality of microorganisms comprising a Trichoderma virens fungus, a Bacillus amyloliquefaciens bacterium, and one or a plurality of mycorrhizae fungi in the vicinity of a plant root in a manner that allows the microorganisms in the composition of matter to colonize said plant root.

The invention includes novel devices and methods for inhibiting or preventing colonization of fluid flow networks by bacteria that have upstream surface motility. In certain aspects, the devices and methods of the invention prevent or minimize undesirable bacterial colonization of medical devices and/or treat or prevent bacterial infections.