Zooming in on the phycosphere: the ecological interface for phytoplankton–bacteria relationships

JR Seymour, SA Amin, JB Raina, R Stocker - Nature microbiology, 2017 - nature.com
By controlling nutrient cycling and biomass production at the base of the food web,
interactions between phytoplankton and bacteria represent a fundamental ecological …

Microbial ecology of mountain glacier ecosystems: biodiversity, ecological connections and implications of a warming climate

S Hotaling, E Hood, TL Hamilton - Environmental microbiology, 2017 - Wiley Online Library
Glacier ecosystems are teeming with life on, beneath, and to a lesser degree, within their icy
masses. This conclusion largely stems from polar research, with less attention paid to …

CheckV assesses the quality and completeness of metagenome-assembled viral genomes

S Nayfach, AP Camargo, F Schulz… - Nature …, 2021 - nature.com
Millions of new viral sequences have been identified from metagenomes, but the quality and
completeness of these sequences vary considerably. Here we present CheckV, an …

Chemotaxis shapes the microscale organization of the ocean's microbiome

JB Raina, BS Lambert, DH Parks, C Rinke, N Siboni… - Nature, 2022 - nature.com
The capacity of planktonic marine microorganisms to actively seek out and exploit
microscale chemical hotspots has been widely theorized to affect ocean-basin scale …

Glacier ice archives nearly 15,000-year-old microbes and phages

ZP Zhong, F Tian, S Roux, MC Gazitúa, NE Solonenko… - Microbiome, 2021 - Springer
Background Glacier ice archives information, including microbiology, that helps reveal
paleoclimate histories and predict future climate change. Though glacier-ice microbes are …

Soil viruses are underexplored players in ecosystem carbon processing

G Trubl, HB Jang, S Roux, JB Emerson, N Solonenko… - …, 2018 - Am Soc Microbiol
Rapidly thawing permafrost harbors∼ 30 to 50% of global soil carbon, and the fate of this
carbon remains unknown. Microorganisms will play a central role in its fate, and their viruses …

GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes

JA Boyd, BJ Woodcroft, GW Tyson - Nucleic Acids Research, 2018 - academic.oup.com
Large-scale metagenomic datasets enable the recovery of hundreds of population genomes
from environmental samples. However, these genomes do not typically represent the full …

Defining the human gut host–phage network through single-cell viral tagging

M Džunková, SJ Low, JN Daly, L Deng, C Rinke… - Nature …, 2019 - nature.com
Viral discovery is accelerating at an unprecedented rate due to continuing advances in
culture-independent sequence-based analyses. One important facet of this discovery is …

Historical contingencies and phage induction diversify bacterioplankton communities at the microscale

RE Szabo, S Pontrelli, J Grilli… - Proceedings of the …, 2022 - National Acad Sciences
In many natural environments, microorganisms decompose microscale resource patches
made of complex organic matter. The growth and collapse of populations on these resource …

Glacier-preserved Tibetan Plateau viral community probably linked to warm–cold climate variations

ZP Zhong, O Zablocki, YF Li, JL Van Etten… - Nature …, 2024 - nature.com
Glaciers archive time-structured information on climates and ecosystems, including
microorganisms. However, the long-term ecogenomic dynamics or biogeography of the …