Off-campus UMass Amherst users: To download campus access dissertations, please use the following link to log into our proxy server with your UMass Amherst user name and password.

Non-UMass Amherst users: Please talk to your librarian about requesting this dissertation through interlibrary loan.

Dissertations that have an embargo placed on them will not be available to anyone until the embargo expires.

Author ORCID Identifier


Campus-Only Access for Five (5) Years

Document Type


Degree Name

Doctor of Philosophy (PhD)

Degree Program


Year Degree Awarded


Month Degree Awarded


First Advisor

Klaus Nusslein

Second Advisor

James F. Holden

Third Advisor

A. Murat Eren

Fourth Advisor

Stephen Petsch

Subject Categories

Environmental Microbiology and Microbial Ecology | Microbial Physiology


Tropical rainforests are large terrestrial carbon sinks that play an essential role in mitigating greenhouse gas emissions. However, these ecosystems are under constant threat from expanding human settlements and agriculture. In particular, Brazil has one of the highest rates of forest loss mainly due to the expansion of cattle pastures. This thesis focused on how conversion of tropical rainforest to cattle pasture influenced the soil microbial communities that are pivotal in carbon cycling. The first study investigated how rainforest-to-pasture conversion altered the total soil microbial community and their functional potential using soil metagenomes and metagenome-assembled genomes (MAGs). A total of 28 MAGs were assembled encompassing 10 phyla, including both dominant and rare biosphere lineages. This study provided unique biological insights into candidate phyla in tropical soil and how deforestation may impact the carbon cycle. The second study focused on how land-use change altered the active soil methane-cycling microorganisms in two geographically distinct locations of the Amazon rainforest. By employing DNA-stable isotope probing on intact soil cores, using heavy 13C-labeled substrates methane, -carbon dioxide, and -sodium acetate, we targeted both the active methanotrophs and methanogens across three different land use types: primary rainforest, cattle pasture, and secondary rainforest. We observed a significant difference in the community composition between land use types for all substrates in Tapajos while Rondonia was only significantly different in the methanogenic substrates. Ultimately, this difference is due to an increase of methanogens and methanogenesis genes in pasture soils, which significantly correlates with the in-field methane gas flux. Unlike previous investigations of the genomic potential, we observed active and abundant methanotrophs in all land-use types. Therefore, we show that active methanotrophy does not decrease in cattle pasture, but rather methanogenesis increases leading to an overall net positive atmospheric methane flux in pastures that contributes to global warming. Additionally, secondary rainforests in both geographic locations were able to recover as methane sinks indicating the potential for reforestation and afforestation to offset greenhouse gas emissions in the tropics due to land use change. This work is critical for informing land management practices and global tropical rainforest conservation.


Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.