Biology subjects

Middelburg, J. J.

Publications and source records attributed to Middelburg, J. J..

3 recordsLinked to original sources

bioRxiv2026

Isotope Labeling Reveals Complex Microbial Interactions during Agaricus bisporus Compost Colonization

Microbial interactions strongly influence carbon and nitrogen flows in mushroom compost, yet their functional roles during Agaricus bisporus colonization remain unresolved. We combined PLFA-SIP and nanoSIMS imaging with ITS amplicon sequencing to follow resource flows and microbial activity across spatial scales. Stable-isotope tracers (13C-glucose and 15N-ammonium) revealed that A. bisporus simultaneously facilitates and suppresses bacterial populations: fungal activity increased glucose assimilation by bacteria yet reduced overall bacterial biomass. NanoSIMS visualized nutrient-rich microenvironments along hyphae where bacterial 13C and 15N assimilation was elevated. Sequencing showed the fungal community to comprise essentially two organisms, A. bisporus and Mycothermus thermophilus, which differ approximately elevenfold in their content of the fungal biomarker C18:2w6,9c. Total fungal PLFA therefore tracks which of the two dominates as much as it tracks fungal biomass. Together these findings reveal coupled fungal-bacterial nutrient processing and show that biomarker-based estimates of fungal biomass require community composition to be known. Multi-scale isotope probing provides a framework for resolving microbial interactions in complex detrital systems.

microbiology↗

bioRxiv2020

Bacterial precursors and unsaturated long-chain fatty acids are biomarkers of North-Atlantic demosponges

Sponges produce distinct fatty acids (FAs) that (potentially) can be used as chemotaxonomic and ecological biomarkers to study endosymbiont-host interactions and the functional ecology of sponges. Here, we present FA profiles of five common habitat-building deep-sea sponges (class Demospongiae, order Tetractinellida), which are classified as high microbial abundance (HMA) species. Geodia hentscheli, G. parva, G. atlantica, G. barretti, and Stelletta rhaphidiophora were collected from boreal and Arctic sponge grounds in the North-Atlantic Ocean. Bacterial FAs dominated in all five species and particularly isomeric mixtures of mid-chain branched FAs (MBFAs, 8- and 9-Me-C16:0 and 10 and 11-Me-C18:0) were found in high abundance (together [≥] 20% of total FAs) aside more common bacterial markers. In addition, the sponges produced long-chain linear, mid- and a(i)-branched unsaturated FAs (LCFAs) with a chain length of 24-28 C atoms and had predominantly the typical {Delta}5,9 unsaturation, although also {Delta}9,19 and (yet undescribed) {Delta}11,21 unsaturations were identified. G. parva and S. rhaphidiophora each produced distinct LCFAs, while G. atlantica, G. barretti, and G. hentscheli produced similar LCFAs, but in different ratios. The different bacterial precursors varied in carbon isotopic composition ({delta}13C), with MBFAs being more enriched compared to other bacterial (linear and a(i)-branched) FAs. We propose biosynthetic pathways for different LCFAs from their bacterial precursors, that are consistent with small isotopic differences found in LCFAs. Indeed, FA profiles of deep-sea sponges can serve as chemotaxonomic markers and support the conception that sponges acquire building blocks from their endosymbiotic bacteria.

biochemistry↗

bioRxiv2020

Reconstructing the diet, trophic level, and migration pattern of Mysticete whales based on baleen isotopic composition.

Baleen from mysticete whales is a well-preserved proteinaceous material that can be used to identify migrations and feeding habits for species whose migration pathways are unknown. Analysis of {delta}13C and {delta}15N from bulk baleen has been used to infer migration patterns for individuals. However, this approach has fallen short of identifying migrations between regions as it is difficult to determine variations in isotopic shifts without temporal sampling of prey items. Here we apply analysis of {delta}15N values of amino acids to five baleen plates belonging to three species, revealing novel insights on trophic position, metabolic state, and migration between regions. Humpback and minke whales had higher reconstructed trophic levels than fin whales (3.4-3.5 versus 2.7-2.9, respectively) as expected due to different feeding specialization. Isotopic niche areas between baleen minima and maxima were well separated, indicating regional resource use for individuals during migration that aligned with isotopic gradients in Atlantic Ocean particulate organic matter. {delta}15N values from phenylalanine confirmed regional separation between the niche areas for two fin whales as migrations occurred and elevated glycine and threonine {delta}15N values revealed physiological changes due to fasting. Simultaneous resolution of trophic level and physiological changes allow for identification of regional migrations in mysticetes.

ecology↗