Common principles and best practices for engineering microbiomes

CE Lawson, WR Harcombe, R Hatzenpichler… - Nature Reviews …, 2019 - nature.com
Despite broad scientific interest in harnessing the power of Earth's microbiomes, knowledge
gaps hinder their efficient use for addressing urgent societal and environmental challenges …

Fungi in aquatic ecosystems

HP Grossart, S Van den Wyngaert, M Kagami… - Nature Reviews …, 2019 - nature.com
Fungi are phylogenetically and functionally diverse ubiquitous components of almost all
ecosystems on Earth, including aquatic environments stretching from high montane lakes …

Microbiome-functionality in anaerobic digesters: a critical review

X Zhang, Y Wang, P Jiao, M Zhang, Y Deng, C Jiang… - Water Research, 2024 - Elsevier
Microbially driven anaerobic digestion (AD) processes are of immense interest due to their
role in the biovalorization of biowastes into renewable energy resources. The function …

Nitrogen recovery through fermentative dissimilatory nitrate reduction to ammonium (DNRA): carbon source comparison and metabolic pathway

Y Zhao, Q Li, Q Cui, SQ Ni - Chemical Engineering Journal, 2022 - Elsevier
The dissimilatory nitrate reduction to ammonium (DNRA) process was known as a short
circuit in nitrogen cycle, a key step in recovering nitrogen from nitrate wastewater, and has …

A review of methods and databases for metagenomic classification and assembly

FP Breitwieser, J Lu, SL Salzberg - Briefings in bioinformatics, 2019 - academic.oup.com
Microbiome research has grown rapidly over the past decade, with a proliferation of new
methods that seek to make sense of large, complex data sets. Here, we survey two of the …

Addressing global ruminant agricultural challenges through understanding the rumen microbiome: past, present, and future

SA Huws, CJ Creevey, LB Oyama, I Mizrahi… - Frontiers in …, 2018 - frontiersin.org
The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi,
methanogenic archaea and phages. These microbes interact closely to breakdown plant …

Genome-based microbial ecology of anammox granules in a full-scale wastewater treatment system

DR Speth, MH in't Zandt, S Guerrero-Cruz… - Nature …, 2016 - nature.com
Partial-nitritation anammox (PNA) is a novel wastewater treatment procedure for energy-
efficient ammonium removal. Here we use genome-resolved metagenomics to build a …

Syntrophic propionate-oxidizing bacteria in methanogenic systems

M Westerholm, M Calusinska… - FEMS Microbiology …, 2022 - academic.oup.com
The mutual nutritional cooperation underpinning syntrophic propionate degradation
provides a scant amount of energy for the microorganisms involved, so propionate …

[HTML][HTML] Biogas production through syntrophic acetate oxidation and deliberate operating strategies for improved digester performance

M Westerholm, J Moestedt, A Schnürer - Applied energy, 2016 - Elsevier
Anaerobic degradation of protein-rich materials has high methane potential and produces
nutrient-rich residue, but requires strategies to avoid ammonia inhibition. A well-adapted …

Chasing the elusive Euryarchaeota class WSA2: genomes reveal a uniquely fastidious methyl-reducing methanogen

MK Nobu, T Narihiro, K Kuroda, R Mei… - The ISME journal, 2016 - academic.oup.com
The ecophysiology of one candidate methanogen class WSA2 (or Arc I) remains largely
uncharacterized, despite the long history of research on Euryarchaeota methanogenesis. To …