Risks to carbon storage from land-use change revealed by peat thickness maps of Peru

This work was funded by NERC (grant ref. NE/R000751/1) to I.T.L., A.H., K.H.R., E.T.A.M., C.M.A., T.R.B., G.D. and E.C.D.G.; Leverhulme Trust (grant ref. RPG-2018-306) to K.H.R., L.E.S.C. and C.E.W.; Gordon and Betty Moore Foundation (grant no. 5439, MonANPeru network) to T.R.B., E.N.H.C. and G.F.; Wildlife Conservation Society to E.N.H.C.; Concytec/British Council/Embajada Británica Lima/Newton Fund (grant ref. 220–2018) to E.N.H.C. and J.D.; Concytec/NERC/Embajada Británica Lima/Newton Fund (grant ref. 001–2019) to E.N.H.C. and N.D.; the governments of the United States (grant no. MTO-069018) and Norway (grant agreement no. QZA-12/0882) to K.H.; and NERC Knowledge Exchange Fellowship (grant ref no. NE/V018760/1) to E.N.H.C.Tropical peatlands are among the most carbon-dense ecosystems but land-use change has led to the loss of large peatland areas, associated with substantial greenhouse gas emissions. To design effective conservation and restoration policies, maps of the location and carbon storage of tropical peatlands are vital. This is especially so in countries such as Peru where the distribution of its large, hydrologically intact peatlands is poorly known. Here field and remote sensing data support the model development of peatland extent and thickness for lowland Peruvian Amazonia. We estimate a peatland area of 62,714 km2 (5th and 95th confidence interval percentiles of 58,325 and 67,102 km2, respectively) and carbon stock of 5.4 (2.6–10.6) PgC, a value approaching the entire above-ground carbon stock of Peru but contained within just 5% of its land area. Combining the map of peatland extent with national land-cover data we reveal small but growing areas of deforestation and associated CO2 emissions from peat decomposition due to conversion to mining, urban areas and agriculture. The emissions from peatland areas classified as forest in 2000 represent 1–4% of Peruvian CO2 forest emissions between 2000 and 2016. We suggest that bespoke monitoring, protection and sustainable management of tropical peatlands are required to avoid further degradation and CO2 emissions.PostprintPeer reviewe

Gametogenesis in the Pacific Oyster Crassostrea gigas: A Microarrays-Based Analysis Identifies Sex and Stage Specific Genes

Background: The Pacific oyster Crassostrea gigas (Mollusca, Lophotrochozoa) is an alternative and irregular protandrous hermaphrodite: most individuals mature first as males and then change sex several times. Little is known about genetic and phenotypic basis of sex differentiation in oysters, and little more about the molecular pathways regulating reproduction. We have recently developed and validated a microarray containing 31,918 oligomers (Dheilly et al., 2011) representing the oyster transcriptome. The application of this microarray to the study of mollusk gametogenesis should provide a better understanding of the key factors involved in sex differentiation and the regulation of oyster reproduction. Methodology/Principal Findings: Gene expression was studied in gonads of oysters cultured over a yearly reproductive cycle. Principal component analysis and hierarchical clustering showed a significant divergence in gene expression patterns of males and females coinciding with the start of gonial mitosis. ANOVA analysis of the data revealed 2,482 genes differentially expressed during the course of males and/or females gametogenesis. The expression of 434 genes could be localized in either germ cells or somatic cells of the gonad by comparing the transcriptome of female gonads to the transcriptome of stripped oocytes and somatic tissues. Analysis of the annotated genes revealed conserved molecular mechanisms between mollusks and mammals: genes involved in chromatin condensation, DNA replication and repair, mitosis and meiosis regulation, transcription, translation and apoptosis were expressed in both male and female gonads. Most interestingly, early expressed male-specific genes included bindin and a dpy-30 homolog and female-specific genes included foxL2, nanos homolog 3, a pancreatic lipase related protein, cd63 and vitellogenin. Further functional analyses are now required in order to investigate their role in sex differentiation in oysters. Conclusions/Significance: This study allowed us to identify potential markers of early sex differentiation in the oyster C. gigas, an alternative hermaphrodite mollusk. We also provided new highly valuable information on genes specifically expressed by mature spermatozoids and mature oocytes

Advancing our understanding of functional genome organisation through studies in the fission yeast

Significant progress has been made in understanding the functional organisation of the cell nucleus. Still many questions remain to be answered about the relationship between the spatial organisation of the nucleus and the regulation of the genome function. There are many conflicting data in the field making it very difficult to merge published results on mammalian cells into one model on subnuclear chromatin organisation. The fission yeast, Schizosaccharomyces pombe, over the last decades has emerged as a valuable model organism in understanding basic biological mechanisms, especially the cell cycle and chromosome biology. In this review we describe and compare the nuclear organisation in mammalian and fission yeast cells. We believe that fission yeast is a good tool to resolve at least some of the contradictions and unanswered questions concerning functional nuclear architecture, since S. pombe has chromosomes structurally similar to that of human. S. pombe also has the advantage over higher eukaryotes in that the genome can easily be manipulated via homologous recombination making it possible to integrate the tools needed for visualisation of chromosomes using live-cell microscopy. Classical genetic experiments can be used to elucidate what factors are involved in a certain mechanism. The knowledge we have gained during the last few years indicates similarities between the genome organisation in fission yeast and mammalian cells. We therefore propose the use of fission yeast for further advancement of our understanding of functional nuclear organisation

Scaling-up engineering biology for enhanced environmental solutions

Synthetic biology (SynBio) offers transformative solutions for addressing environmental challenges by engineering organisms capable of degrading pollutants, enhancing carbon sequestration, and valorizing waste (Figure 1). These innovations hold the potential to revolutionize bioremediation strategies, ecosystem restoration, and sustainable environmental management. (1) Advances in SynBio, including automation, precise manipulation of genetic material, (2) and design of semisynthetic organisms with enhanced capabilities, can improve the efficiency of microbes for eliminating pollutants such as hydrocarbons and plastics or extracting valuable resources from the environment. (3) Genome editing technologies, such as CRISPR-Cas9, allows the editing of genomes with unprecedented accuracy, facilitating the development of organisms with desired traits or functions. (4) Furthermore, SynBio encompasses the engineering of metabolic enzymes within organisms, leading to the design of microbial factories capable of degrading complex and persistent chemicals, and converting waste to valuable resources. (5) These advancements also facilitate the manipulation of bacterial social behaviors, offering the capacity for tunable control at the multicellular level and engineered biofilms. (5

Denial of long-term issues with agriculture on tropical peatlands will have devastating consequences

Non peer reviewe

Variation in Vegetation and Ecosystem Carbon Stock Due to the Conversion of Disturbed Forest to Oil Palm Plantation in Peruvian Amazonia

Peruvian national and regional plans promoting oil palm have prompted a rapid expansion of the crop in the Amazonian region. This expansion has taken place primarily at the expense of forest, both undisturbed and disturbed. Assessments of carbon emissions from forest-to-oil palm conversion have essentially been confined to Southeast Asia, and research on Peruvian Amazonian forests has mainly targeted undisturbed sites. This study characterizes the vegetation structure and composition of disturbed forests and smallholder oil palm plantations and evaluates the change in ecosystem (that is, phytomass and soil) carbon stocks associated with forest-to-oil palm conversion. Inventories were conducted in four degraded forest sites neighboring six oil palm plantation sites in Ucayali. Time-averaged carbon stocks over the 30-year oil palm rotation were computed from models developed upon the sampled chronosequence (1 to 28 years old). Disturbed forests harbored species typical of primary forests, pioneer species and gaps opportunistic species. Their tree basal area (18.7 ± 1.4 m2 ha−1) and above-ground C stock (71.3 ± 4.2 Mg C ha−1) were, respectively, 50 and 60% of the values of undisturbed forests from the literature. The growth curve for oil palm above-ground biomass was consistently below models developed for plantations in Indonesia. Thirty-year time-averaged ecosystem C stock (Mg C ha−1) in oil palm plantations (78.2 ± 2.0) represented 55% of the stock in disturbed forest (140.9 ± 5.8), resulting in a 62.7 ± 6.1 loss from such conversion. These results reinforce recommendations to redirect oil palm expansion toward low-carbon degraded lands, sparing disturbed and undisturbed forests

Degradation-driven changes in fine root carbon stocks, productivity, mortality, and decomposition rates in a palm swamp peat forest of the Peruvian Amazon

Amazon palm swamp peatlands are major carbon (C) sinks and reservoirs. In Peru, this ecosystem is widely threatened owing to the recurrent practice of cutting Mauritia flexuosa palms for fruit harvesting. Such degradation could significantly damage peat deposits by altering C fluxes through fine root productivity, mortality, and decomposition rates which contribute to and regulate peat accumulation. Along a same peat formation, we studied an undegraded site (Intact), a moderately degraded site (mDeg) and a heavily degraded site (hDeg) over 11 months. Fine root C stocks and fluxes were monthly sampled by sequential coring. Concomitantly, fine root decomposition was investigated using litter bags. In the experimental design, fine root stocks and dynamics were assessed separately according to vegetation type (M. flexuosa palm and other tree species) and M. flexuosa age class. Furthermore, results obtained from individual palms and trees were site-scaled by using forest composition and structure