Limited understanding of interactions between biogeochemistry and biodiversity represents a major obstacle to advancing empirical and theoretical ecology. To address this obstacle, we take a seldom used perspective, that is, we explore what is unknown about the patterns and processes of biogeochemistry, biodiversity and their inter-relationship. We draw widely from research on temperate forest ecosystems but use primarily the long-term data sets and experiments of a well studied forest ecosystem and LTER site: the Hubbard Brook Experimental Forest, New Hampshire. Specifically, we focus on the biogeochemistry of carbon, nitrogen, phosphorus and calcium, addressing what is unknown about how these basic biogeochemical cycles affect and are affected by biodiversity in the microbial, brown (forest floor), green (foliar) and blue (stream and pond) food webs. We address whether current sampling schemes (i.e., spatial and temporal scales) and concepts (e.g., pools, fluxes, species, functional groups) are those best suited to the integration of biogeochemistry and biodiversity, and we present testable hypotheses aimed at characterizing and quantifying biogeochemistry-biodiversity interactions and feedbacks over time and space.
The following are major gaps in knowledge of ecosystem processes that currently preclude integration of biogeochemistry and biodiversity. The hydropedologic template is the foundation of ecosystem processes, but variation in biogeochemistry by soil units is largely unknown. This template sustains organisms from producers to decomposers that make up local biodiversity, but past research has produced landscape-level averages that may poorly represent the spatial heterogeneity that sustains system biodiversity. Each element assessed can affect some aspect of biodiversity, but in nearly all cases, the mechanism(s) by which these elements act alone or together to affect diversity is unknown, as are feedbacks between heterotroph activity and element cycling. Biodiversity is greatest in the microbial and brown food webs, but concomitantly taxonomic identities, population dynamics, species interactions and functional diversity are less well understood for these food webs – those most closely associated with energy flow and materials cycling. Additional knowledge gaps are identified, and we provide examples of focused monitoring, experiments and modeling that can be used to close some of these gaps. We conclude by presenting a novel view of ecosystem structure, as a mosaic of spatially nested trophic networks, which we may aid in the integration of biogeochemistry and biodiversity.