Plant pangenomes for crop improvement, biodiversity and evolution

Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as mapping the molecular basis of trait diversity in domesticated plants or inquiries into the origin of evolutionary innovations in flowering plants millions of years ago. The transformative technological progress of DNA sequencing in the past two decades has enabled researchers to sequence ever more genomes with greater ease. Pangenomes - complete sequences of multiple individuals of a species or higher taxonomic unit - have now entered the geneticists' toolkit. The genomes of crop plants and their wild relatives are being studied with translational applications in breeding in mind. But pangenomes are applicable also in ecological and evolutionary studies, as they help classify and monitor biodiversity across the tree of life, deepen our understanding of how plant species diverged and show how plants adapt to changing environments or new selection pressures exerted by human beings.

Biogeochemical processes controlling the dynamics of dissolved organic matter in streams in the Shirakami Mountains, Japan

The Shirakami Mountain range, including the largest primeval beech forest in East-Asia, is undergoing ecological change. Dissolved organic matter (DOM) plays an important role in nutrient and material cycling in forest ecosystems. Because the quality of DOM varies based on its origin and diagenetic and runoff processes, changes in the environment surrounding DOM can be rapidly detected by monitoring its quality. Herein, concentrations and fluorescence composition of DOM at 14 sites in 13 streams in the Shirakami Mountain range were monitored monthly for over 2 years, excluding winter (December-March), to gain insight into the catchment hydrological and soil characteristics affecting DOM concentrations and composition in stream water. Based on the pattern of temporal changes in fluorescent component composition, monitoring sites were categorized into four groups (streams with small catchments, large catchments, catchments facing the Sea of Japan, and open waters in the catchment) with similar catchment characteristics affecting DOM dynamics. Multiple linear regression analysis showed that DOM concentrations in each group could be attributed to rainfall on the survey date, short-term (1-2 days) rainfall, midterm (~1 month) accumulated rainfall, midterm (7-11 days) accumulated temperature, and catchment characteristics as explanatory variables. The degree of influence of these variables differed among the four groups. The results of this study show that grouping streams according to catchment hydrological characteristics can help identify the impact of climate and environmental change on DOM dynamics in stream water.

Marine Pelagic Ecosystem Responses to Climate Variability and Change

The marine coastal region makes up just 10% of the total area of the global ocean but contributes nearly 20% of its total primary production and over 80% of fisheries landings. Unicellular phytoplankton dominate primary production. Climate variability has had impacts on various marine ecosystems, but most sites are just approaching the age at which ecological responses to longer term, unidirectional climate trends might be distinguished. All five marine pelagic sites in the US Long Term Ecological Research (LTER) network are experiencing warming trends in surface air temperature. The marine physical system is responding at all sites with increasing mixed layer temperatures and decreasing depth and with declining sea ice cover at the two polar sites. Their ecological responses are more varied. Some sites show multiple population or ecosystem changes, whereas, at others, changes have not been detected, either because more time is needed or because they are not being measured.

OUP accepted manuscript

In this article marking the 40th anniversary of the US National Science Foundation's Long Term Ecological Research (LTER) Network, we describe how a long-term ecological research perspective facilitates insights into an ecosystem's response to climate change. At all 28 LTER sites, from the Arctic to Antarctica, air temperature and moisture variability have increased since 1930, with increased disturbance frequency and severity and unprecedented disturbance types. LTER research documents the responses to these changes, including altered primary production, enhanced cycling of organic and inorganic matter, and changes in populations and communities. Although some responses are shared among diverse ecosystems, most are unique, involving region-specific drivers of change, interactions among multiple climate change drivers, and interactions with other human activities. Ecosystem responses to climate change are just beginning to emerge, and as climate change accelerates, long-term ecological research is crucial to understand, mitigate, and adapt to ecosystem responses to climate change.