Pollinators are a key component of global biodiversity, providing vital ecosystem services to crops and wild plants. There is clear evidence of recent declines in both wild and domesticated pollinators, and parallel declines in the plants that rely upon them. Here we describe the nature and extent of reported declines, and review the potential drivers of pollinator loss, including habitat loss and fragmentation, agrochemicals, pathogens, alien species, climate change and the interactions between them. Pollinator declines can result in loss of pollination services which have important negative ecological and economic impacts that could significantly affect the maintenance of wild plant diversity, wider ecosystem stability, crop production, food security and human welfare.

/pdf/global-pollinator-declines-trends-impacts-and-drivers-5gfi4zur4k.pdf

Global pollinator declines: trends, impacts and drivers.

Climate change 2014 - Synthesis Report

Viruses exist wherever life is found. They are a major cause of mortality, a driver of global geochemical cycles and a reservoir of the greatest genetic diversity on Earth. In the oceans, viruses probably infect all living things, from bacteria to whales. They affect the form of available nutrients and the termination of algal blooms. Viruses can move between marine and terrestrial reservoirs, raising the spectre of emerging pathogens. Our understanding of the effect of viruses on global systems and processes continues to unfold, overthrowing the idea that viruses and virus-mediated processes are sidebars to global processes.

Viruses in the sea

A census of the biomass on Earth is key for understanding the structure and dynamics of the biosphere. However, a global, quantitative view of how the biomass of different taxa compare with one another is still lacking. Here, we assemble the overall biomass composition of the biosphere, establishing a census of the ≈550 gigatons of carbon (Gt C) of biomass distributed among all of the kingdoms of life. We find that the kingdoms of life concentrate at different locations on the planet; plants (≈450 Gt C, the dominant kingdom) are primarily terrestrial, whereas animals (≈2 Gt C) are mainly marine, and bacteria (≈70 Gt C) and archaea (≈7 Gt C) are predominantly located in deep subsurface environments. We show that terrestrial biomass is about two orders of magnitude higher than marine biomass and estimate a total of ≈6 Gt C of marine biota, doubling the previous estimated quantity. Our analysis reveals that the global marine biomass pyramid contains more consumers than producers, thus increasing the scope of previous observations on inverse food pyramids. Finally, we highlight that the mass of humans is an order of magnitude higher than that of all wild mammals combined and report the historical impact of humanity on the global biomass of prominent taxa, including mammals, fish, and plants.

https://www.pnas.org/content/pnas/115/25/6506.full.pdf

The biomass distribution on Earth

Home PURPOSE OF THE CENTER: To develop the center to address state-of-the-art research, create innovating educational programs, and support technology transfers using commercially viable results to assist the Army Research Laboratory to develop the next generation Future Combat System in the telecommunications sector that assures prevention of perceived threats, and Non Line of Sight/Beyond Line of Sight lethal support.

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Encapsulated in sediments: eDNA deciphers the ecosystem history of one of the most polluted European marine sites.

Changes in coral forest microbiomes predict the impact of marine heatwaves on habitat-forming species down to mesophotic depths.

Environmental metagenomics is a challenging approach that is exponentially spreading in the scientific community to investigate taxonomic diversity and possible functions of the biological components. The massive amount of sequence data produced, often endowed with rich environmental metadata, needs suitable computational tools to fully explore the embedded information. Bioinformatics plays a key role in providing methodologies to manage, process and mine molecular data, integrated with environmental metagenomics collections. One such relevant example is represented by the Tara Ocean Project. We considered the Tara 16S miTAGs released by the consortium, representing raw sequences from a shotgun metagenomics approach with similarities to 16S rRNA genes. We generated assembled 16S rDNA sequences, which were classified according to their lengths, the possible presence of chimeric reads, the putative taxonomic affiliation. The dataset was included in GLOSSary (the GLobal Ocean 16S Subunit web accessible resource), a bioinformatics platform to organize environmental metagenomics data. The aims of this work were: i) to present alternative computational approaches to manage challenging metagenomics data; ii) to set up user friendly web-based platforms to allow the integration of environmental metagenomics sequences and of the associated metadata; iii) to implement an appropriate bioinformatics platform supporting the analysis of 16S rDNA sequences exploiting reference datasets, such as the SILVA database. We organized the data in a next-generation NoSQL “schema-less” database, allowing flexible organization of large amounts of data and supporting native geospatial queries. A web interface was developed to permit an interactive exploration and a visual geographical localization of the data, either raw miTAG reads or 16S contigs, from our processing pipeline. Information on unassembled sequences is also available. The taxonomic affiliations of contigs and miTAGs, and the spatial distribution of the sampling sites and their associated sequence libraries, as they are contained in the Tara metadata, can be explored by a query interface, which allows both textual and visual investigations. In addition, all the sequence data were made available for a dedicated BLAST-based web application alongside the SILVA collection. GLOSSary provides an expandable bioinformatics environment, able to support the scientific community in current and forthcoming environmental metagenomics analyses.

/pdf/glossary-the-global-ocean-16s-subunit-web-accessible-bugg3jpf8m.pdf

GLOSSary: the GLobal Ocean 16S subunit web accessible resource.

Section 2 update: Degradation and turnover of extracellular DNA in marine sediments

Metagenomic sequencing of nucleic acids from environmental or other complex samples can be successfully used as a powerful tool for environmental quality assessment. Being a culture-independent approach, it does not rely on the presence or absence of specific organisms or genes, and can even identify novel organisms. When focused on viruses, metagenomics can help to shed light on their involvement in ecosystem functioning, due to their dependence on their hosts and their ability to respond quickly to environmental changes. Moreover, viral metagenomics can show the impact of contamination on different natural ecosystems, highlighting putative sources and potential pathogens.

Cinzia Corinaldesi

Papers

Encapsulated in sediments: eDNA deciphers the ecosystem history of one of the most polluted European marine sites.

Changes in coral forest microbiomes predict the impact of marine heatwaves on habitat-forming species down to mesophotic depths.

GLOSSary: the GLobal Ocean 16S subunit web accessible resource.

Section 2 update: Degradation and turnover of extracellular DNA in marine sediments

Viral metagenomics: a new and complementary tool for environmental quality assessment