Land-Use Change, Soil Process and Trace Gas Fluxes in the Brazilian Amazon Basin

We measured changes in key soil processes and the fluxes of CO2, CH4 and N2O associated with the conversion of tropical rainforest to pasture in Rondonia, a state in the southwest Amazon that has experienced rapid deforestation, primarily for cattle ranching, since the late 1970s. These measurements provide a comprehensive quantitative picture of the nature of surface soil element stocks, C and nutrient dynamics, and trace gas fluxes between soils and the atmosphere during the entire sequence of land-use change from the initial cutting and burning of native forest, through planting and establishment of pasture grass and ending with very old continuously-pastured land. All of our work is done in cooperation with Brazilian scientists at the Centro de Energia Nuclear na Agricultura (CENA) through an extant official bi-lateral agreement between the Marine Biological Laboratory and the University of Sao Paulo, CENA's parent institution

Soil warming alters nitrogen cycling in a New England forest : implications for ecosystem function and structure

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Oecologia 168 (2012): 819-828, doi:10.1007/s00442-011-2133-7.Global climate change is expected to affect terrestrial ecosystems in a variety of ways. Some of the more well-studied effects include the biogeochemical feedbacks to the climate system that can either increase or decrease the atmospheric load of greenhouse gases such as carbon dioxide and nitrous oxide. Less well-studied are the effects of climate change on the linkages between soil and plant processes. Here, we report the effects of soil warming on these linkages observed in a large field manipulation of a deciduous forest in southern New England, USA, where soil was continuously warmed 5°C above ambient for 7 years. Over this period, we have observed significant changes to the nitrogen cycle that have the potential to affect tree species composition in the long term. Since the start of the experiment, we have documented a 45% average annual increase in net nitrogen mineralization and a three-fold increase in nitrification such that in years 5 through 7, 25% of the nitrogen mineralized is then nitrified. The warming-induced increase of available nitrogen resulted in increases in the foliar nitrogen content and the relative growth rate of trees in the warmed area. Acer rubrum (red maple) trees have responded the most after 7 years of warming, with the greatest increases in both foliar nitrogen content and relative growth rates. Our study suggests that considering species-specific responses to increases in nitrogen availability and changes in nitrogen form is important in predicting future forest composition and feedbacks to the climate system.This work was supported by the National Institute for Climate Change Research (DOE-DE-FCO2-06-ER64157), DOE BER (DE-SC0005421) and the Harvard Forest Long-Term Ecological Research program (NSF-DEB-0620443)

CO2 and CH4 exchanges between land ecosystems and the atmosphere in northern high latitudes over the 21st century

Author Posting. © American Geophysical Union, 2006. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 33 (2006): L17403, doi:10.1029/2006GL026972.Terrestrial ecosystems of the northern high latitudes (above 50oN) exchange large amounts of CO2 and CH4 with the atmosphere each year. Here we use a process-based model to estimate the budget of CO2 and CH4 of the region for current climate conditions and for future scenarios by considering effects of permafrost dynamics, CO2 fertilization of photosynthesis and fire. We find that currently the region is a net source of carbon to the atmosphere at 276 Tg C yr-1. We project that throughout the 21st century, the region will most likely continue as a net source of carbon and the source will increase by up to 473 Tg C yr-1 by the end of the century compared to the current emissions. However our coupled carbon and climate model simulations show that these emissions will exert relatively small radiative forcing on global climate system compared to large amounts of anthropogenic emissions.This study was supported by a NSF Biocomplexity (ATM-0120468) and ARCSS programs; the NASA Land Cover and Land Use Change and EOS Interdisciplinary Science (NNG04GJ80G) programs; and by funding from MIT Joint Program on the Science and Policy of Global Change, which is supported by a consortium of government, industry and foundation sponsors

The methanol dehydrogenase gene, mxaF, as a functional and phylogenetic marker for proteobacterial methanotrophs in natural environments

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in PLoS ONE 8 (2013): e56993, doi:10.1371/journal.pone.0056993.The mxaF gene, coding for the large (α) subunit of methanol dehydrogenase, is highly conserved among distantly related methylotrophic species in the Alpha-, Beta- and Gammaproteobacteria. It is ubiquitous in methanotrophs, in contrast to other methanotroph-specific genes such as the pmoA and mmoX genes, which are absent in some methanotrophic proteobacterial genera. This study examined the potential for using the mxaF gene as a functional and phylogenetic marker for methanotrophs. mxaF and 16S rRNA gene phylogenies were constructed based on over 100 database sequences of known proteobacterial methanotrophs and other methylotrophs to assess their evolutionary histories. Topology tests revealed that mxaF and 16S rDNA genes of methanotrophs do not show congruent evolutionary histories, with incongruencies in methanotrophic taxa in the Methylococcaceae, Methylocystaceae, and Beijerinckiacea. However, known methanotrophs generally formed coherent clades based on mxaF gene sequences, allowing for phylogenetic discrimination of major taxa. This feature highlights the mxaF gene’s usefulness as a biomarker in studying the molecular diversity of proteobacterial methanotrophs in nature. To verify this, PCR-directed assays targeting this gene were used to detect novel methanotrophs from diverse environments including soil, peatland, hydrothermal vent mussel tissues, and methanotroph isolates. The placement of the majority of environmental mxaF gene sequences in distinct methanotroph-specific clades (Methylocystaceae and Methylococcaceae) detected in this study supports the use of mxaF as a biomarker for methanotrophic proteobacteria.This work was supported in part by grants from the U.S. National Science Foundation Ecosystems Studies program (awards # DEB9708092 and DEB0089738)

Phylogenetic tree of environmental <i>mxaF</i> gene sequences detected in this study.

<p>Phylogenetic tree based on MP analyses of environmental partial <i>mxaF</i> nucleotide sequences (∼513 bp) detected in this study (in bold) in comparison with their close relatives, with <i>Solibacter usitatus</i> Ellin6076 as outgroup. All <i>mxaF</i> sequences were obtained using primer pair F1003 and R1561, except for the 13 putative symbiont <i>mxaF</i> genes from <i>Bathymodiolus azoricus</i> and <i>B. puteoserpentis,</i> which were obtained using primer pair F1003degen and R1561degen. Accession numbers of sequences downloaded from GenBank are indicated in parentheses. Bootstrap values from 1,000 replicates are indicated at the nodes of branches (if >50). Clone sequences are labeled P_C, pine soil (control); P_F, pine soil (fertilized); H_F, hardwood soil (fertilized); Sphag, <i>Sphagnum</i> moss; HBHA, Halls Brook Holding Area; RB, Rainbow; LS, Lucky Strike; LO, Logatchev, followed by clone number (#).Methanotrophs found in the three bacterial families (Methylococcaceae, Methylcystaceae and Beijerinckiaceae) are shaded. Bootstrap values from 1,000 replicates are indicated at the nodes of branches (if >50). The scale bar represents the number of nucleotide changes.</p

PCR Primers sets used in this study.

<p>PCR Primers sets used in this study.</p

Simplified phylogenetic tree of methanotrophs and their close relatives based on <i>mxaF</i> nucleotide sequences from GenBank database.

<p>Unrooted phylogenetic tree based on maximum parsimony (MP) analysis of known proteobacterial partial <i>mxaF</i> and <i>xoxF</i>/<i>xoxF</i>-like nucleotide sequences (∼513 bp) from GenBank and the <i>mxaF</i> nucleotide sequences (in bold) of <i>Methylomonas rubra</i> and <i>Methylobacter luteus</i> sequenced in this study. The ADH gene of <i>Solibacter usitatus</i> Ellin 6076 was used as outgroup. Accession numbers of sequences downloaded from GenBank are indicated in parentheses. Bootstrap values from 1,000 replicates are indicated at the nodes of branches (if >50). The three bacterial families containing methanotrophs (Methylococcaceae, Methylocystaceae and methanotrophic members of the Beijerinckiaceae) are indicated by shaded clusters and the other alphaproteobacterial and betaproteobacterial methylotrophs are delineated by lines. The identity of <i>mxaF</i> and <i>mxaF</i>-like sequences from the “<i>Methylobacterium</i> cluster (within cluster 2)”, “Mainly <i>Hyphomicrobium</i> (Cluster 3)”, “β-proteobacterial methylotrophs (Cluster 5)”, and “<i>xoxF/xoxF</i>-like genes” is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056993#pone-0056993-t002" target="_blank">Table 2</a>. The scale bar represents the number of nucleotide changes. The complete phylogenetic tree of methanotrophs and their close relatives based on <i>mxaF</i> nucleotide sequences is shown in Supplement S1.</p

Congruency tests between <i>mxaF</i> and 16S rRNA gene nucleotide sequences of methanotrophs from GenBank database.

<p>Phylogenetic trees for congruency tests based on maximum likelihood (ML) analysis of <i>mxaF</i> (∼513 bp) and 16S rRNA gene nucleotide sequences (∼1471 bp) from methanotrophs in GenBank, including the <i>mxaF</i> nucleotide sequences of <i>Methylomonas rubra</i> and <i>Methylobacter luteus</i> sequenced in this study. The ADH gene of <i>Solibacter usitatus</i> Ellin 6076 was used as outgroup. Methanotrophs (in the Methylococcaceae, Methylocystaceae and Beijerinckiaceae) are indicated by shaded clusters. Accession numbers of <i>mxaF</i> and 16S rRNA gene sequences downloaded from GenBank are indicated in parentheses. Bootstrap values from 1,000 replicates are indicated at the nodes of branches (if >50). The scale bar represents the number of nucleotide changes.</p

Taxa included (but not shown) in the phylogenetic analyses for Fig. 2.

<p>Taxa included (but not shown) in the phylogenetic analyses for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0056993#pone-0056993-g002" target="_blank">Fig. 2</a>.</p