Pervasive gaps in Amazonian ecological research

Biodiversity loss is one of the main challenges of our time, and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space. While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes, vast areas of the tropics remain understudied. In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity, but it remains among the least known forests in America and is often underrepresented in biodiversity databases. To worsen this situation, human-induced modifications may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge, it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost

The Fungal Pathogen <em>Moniliophthora perniciosa</em> Has Genes Similar to Plant PR-1 That Are Highly Expressed during Its Interaction with Cacao

<div><p>The widespread SCP/TAPS superfamily (SCP/Tpx-1/Ag5/PR-1/Sc7) has multiple biological functions, including roles in the immune response of plants and animals, development of male reproductive tract in mammals, venom activity in insects and reptiles and host invasion by parasitic worms. Plant Pathogenesis Related 1 (PR-1) proteins belong to this superfamily and have been characterized as markers of induced defense against pathogens. This work presents the characterization of eleven genes homologous to plant <em>PR-1</em> genes, designated as <em>MpPR-1</em>, which were identified in the genome of <em>Moniliophthora perniciosa</em>, a basidiomycete fungus responsible for causing the devastating witches' broom disease in cacao. We describe gene structure, protein alignment and modeling analyses of the MpPR-1 family. Additionally, the expression profiles of <em>MpPR-1</em> genes were assessed by qPCR in different stages throughout the fungal life cycle. A specific expression pattern was verified for each member of the <em>MpPR-1</em> family in the conditions analyzed. Interestingly, some of them were highly and specifically expressed during the interaction of the fungus with cacao, suggesting a role for the MpPR-1 proteins in the infective process of this pathogen. Hypothetical functions assigned to members of the <em>MpPR-1</em> family include neutralization of plant defenses, antimicrobial activity to avoid competitors and fruiting body physiology. This study provides strong evidence on the importance of <em>PR-1-like</em> genes for fungal virulence on plants.</p> </div

Comparison of MpPR-1 and SCP/TAPS proteins of representative organisms.

<p>(A) Domain arrangement of SCP/TAPS proteins. Hydrophobic signal peptides are shown in black and SCP/TAPS domains are represented in blue. The numbers on the right show the size of each protein. Large N-terminal and C-terminal expansions are observed in MpPR-1b and MpPR-1g, respectively. (B) Alignment of the conserved domain of SCP/TAPS proteins. In general, the SCP/TAPS superfamily members show similarities only over the SCP/TAPS domain. Conserved residues (100% of identity) are shown in blue and semi-conserved residues (at least 60% of identity) in green. Putative active site residues are highlighted in red and cysteines in yellow. Secondary structure elements are shown above the alignment (arrow: β-sheets; helix: α-helixes). P14, tomato PR-1 (GenBank P04284); RBT4, repressed by TUP1 from <i>Candida albicans</i> (GenBank AAG09789); Tex31, SCP/TAPS from the mollusk <i>Conus textile</i> (GenBank CAD36507); Na-ASP-2, <i>Necator americanus</i> secreted protein (GenBank AAP41952); GliPR-1, human glioma PR-1 protein (GenBank P48060); SC7, SCP/TAPS from the basidiomycete <i>Schizophyllum commune</i> (GenBank P35794).</p

Transcriptional profile of <i>MpPR-1</i> family members throughout the <i>M. perniciosa</i> life cycle.

<p>Each <i>MpPR-1</i> gene has a distinct expression profile during fungal development. “Monokaryotic” and “Dikaryotic” hyphae represent the two mycelial stages (biotrophic and necrotrophic) grown under <i>in vitro</i> conditions. “Green broom” and “dry broom” correspond to the biotrophic and necrotrophic stages of <i>M. perniciosa</i>, respectively, during its interaction with cacao. Analyses were performed by qPCR and the <i>M. perniciosa β-actin</i> gene was used as endogenous control to normalize data. Error bars represent standard deviations determined with two biological replicates. Representative drawings of the conditions analyzed are shown on the top.</p

Genomic organization and transcriptional profile of the <i>MpPR-1</i> gene cluster found in <i>M. perniciosa</i>.

<p>The <i>MpPR-1c</i>, <i>MpPR-1d</i> and <i>MpPR-1j</i> genes are arranged <i>in tandem</i> over a region of approximately 5 kbp. Analysis of the WBD RNA-seq Atlas shows the expression profile of these <i>MpPR-1</i> genes in different conditions (green broom – <i>in planta</i> development of the biotrophic monokaryotic hyphae; monokaryotic mycelium; dikaryotic mycelium; basidiomata and basidiospores). Data were visualized using the Integrative Genomics Viewer <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045929#pone.0045929-Robinson1" target="_blank">[62]</a>. The black coverage plot shows cumulative RNA-seq read coverage along the transcripts in all different conditions. Note that these genes were named according to the order they were identified in the fungal genome, and the nomenclature does not necessarily reflect their relative localization in the genome.</p

Homology modeling of MpPR-1 proteins.

<p>(A) Ribbon stick representation showing the folding of eleven MpPR-1 proteins and three SCP/TAPS proteins used to obtain these models. The putative residues forming the catalytic site are highlighted in dark blue (histidines) and light blue (glutamic acids). Note the presence of an additional protein module in MpPR-1b and MpPR-1g. These modules respectively correspond to the N-terminal and C-terminal extensions observed in these proteins. (B) MpPR-1b, MpPR-1c, MpPR-1d, MpPR-1e, MpPR-1h and MpPR-1j have the four putative active site residues of the SCP/TAPS domain. (C) These residues are partially or completely absent in MpPR-1a, MpPR-1f, MpPR-1g, MpPR-1i and MpPR-1k.</p

Domains identified in the MpPR-1g protein.

<p>In addition to the SCP/TAPS domain, this protein has a KEKE motif in its C-terminal extension. This motif is known to mediate the interaction with other proteins or ions.</p

Draft genome sequence of Kocuria sp. SM24M-10 isolated from coral mucus

Here, we describe the genomic features of the Actinobacteria Kocuria sp. SM24M-10 isolated from mucus of the Brazilian endemic coral Mussismilia hispida. The sequences are available under accession number LDNX01000000 (http://www.ncbi.nlm.nih.gov/nuccore/LDNX00000000). The genomic analysis revealed interesting information about the adaptation of bacteria to the marine environment (such as genes involved in osmotic and oxidative stress) and to the nutrient-rich environment provided by the coral mucus. Keywords: Kocuria sp. SM24M-10, Coral mucus, Osmotic stress, Oxidative stres