Biology subjects

de Boer, W.

Publications and source records attributed to de Boer, W..

4 recordsLinked to original sources

bioRxiv2024

Acidotolerant soil nitrite oxidiser 'Candidatus Nitrobacter laanbroekii' NHB1 alleviates constraints on growth of acidophilic soil ammonia oxidisers

Nitrobacter strain NHB1 is a nitrite-oxidising bacterium previously co-enriched with the neutrophilic ammonia-oxidising bacterium Nitrosospira AHB1, a consortium that nitrifies under acidic conditions. Here we characterise the growth of isolated Nitrobacter strain NHB1 as a function of pH and nitrite (NO2-) concentration, and its influence on the activity of acidophilic soil ammonia-oxidising archaea (AOA) in co-culture. NHB1 is acidotolerant and grows optimally at pH 6.0 (range 5.0 - 7.5) at initial NO2- concentrations of 500 {micro}M. However, the optimum decreases to pH 5.0 at lower initial NO2- concentrations closer to those found in soil, with detectable growth down to pH 3.5. NHB1 has a comparatively high affinity for NO2- with an apparent-half-saturation constant (54 {micro}M) one order of magnitude lower than its closest relative, the neutrophilic strain Nitrobacter hamburgensis X14. In co-culture, NHB1 enhances the growth of acidophilic AOA. Specifically, Nitrosotalea devaniterrae Nd1 and Nitrosotalea sinensis Nd2 are sensitive to NO2--derived compounds and only oxidise [~]200-300 {micro}M ammonia (NH3) in batch cultures. However, in co-culture with NHB1, pH ranges were lowered by [~]0.5 pH units and both strains could oxidise up to 2.7-2.9 mM NH3, only limited by buffering capacity. NHB1 possesses a cyanase facilitating reciprocal cross-feeding via generating cyanate-derived NH3 and utilising AOA-derived NO2-. Removal of NO2- is likely crucial for nitrifier growth in acidic soils and this study highlights the importance of considering substrate and metabolic product concentrations when characterising physiology. Genome analysis reveals that NHB1 is distinct from validated species and the name Nitrobacter laanbroekii is proposed.

microbiology↗

bioRxiv2021

Assessing the role of fungal diversity in decomposition: A meta-analysis

Fungi play an important role in carbon - and nutrient cycling. It is, however, unclear if diversity of fungi is essential to fulfill this role. With this meta-analysis, we aim to understand the relationship between fungal diversity and decomposition of plant materials (leaf litter and wood) in terrestrial and aquatic environments. The selection criteria for papers were the presence of a fungal diversity gradient and quantification of decomposition as mass loss. In total 40 papers met the selection criteria. We hypothesized that increase of fungal species will result in stronger decomposition, especially in species poor communities. Both artificial inoculated and naturally assembled fungal communities were included in the analysis in order to assess whether manipulated experiments are representative for field situations. We found a significant positive effect of increased fungal diversity on decomposition. However, in manipulated experiments this relationship was only positive when a control treatment of one fungus was compared with multispecies communities. This relationship became negative when comparisons of higher initial richness (at least two fungal species as "control") were included. In contrast, under natural field conditions increased fungal diversity coincided with increased decomposition. This suggests that manipulated experiments are not representative for field situations. Possible reasons for this are discussed. Yet, both in manipulated and field experiments, environmental factors can influence diversity - decomposition relationships as indicated by a negative relationship of increasing C:N ratio on the effect of fungal diversity on decomposition. Overall, our results show that fungal diversity can have an important role in decomposition, but that design of experiments (manipulated or field) and quality of the plant material should be taken into account for interpretation of this diversity-functioning relationship.

microbiology↗

bioRxiv2020

Effect of nitrogen on fungal growth efficiency

The contribution of fungi to carbon (C) and nitrogen (N) cycling is related to their growth efficiency (amount of biomass produced per unit of substrate utilized). The concentration and availability of N influences the activity and growth efficiency of saprotrophic fungi. When N is scarce in soils, fungi have to invest more energy to obtain soil N, which could result in lower growth efficiencies. Yet, the effect of N on growth efficiencies of individual species of fungi in soil has not been studied extensively. In this study we investigated the influence of different concentrations of mineral N on the growth efficiency of two common soil fungi, Trichoderma harzanium and Mucor hiemalis in a soil-like environment. We hypothesized that a higher N availability will coincide with higher biomass production and growth efficiency. To test this, we measured fungal biomass production as well as the respiration fluxes in sand microcosms amended with cellobiose and mineral N at different C:N ratios. We found that for both fungal species lower C:N ratios resulted in the highest biomass production as well as the highest growth efficiency. This may imply that when N is applied concurrently with a degradable C source, a higher amount of N will be temporarily immobilized into fungal biomass.

ecology↗

bioRxiv2020

Identification and antimicrobial properties of bacteria isolated from naturally decaying wood

Research on wood decay in forest ecosystems has traditionally focused on wood-rot fungi, which lead the decay process through attack of the lignocellulose complex. The role of bacteria, which can be highly abundant, is still unclear. Wood-inhabiting bacteria are thought to be nutritionally dependent on decay activities of wood-rot fungi. Therefore, we hypothesized that these bacteria are not antagonistic against wood-rot fungi whereas antagonistic activity against other bacteria may be high (resource competition). This was examined for decaying wood in temperate forests. We found that the abundance of cultivable bacteria in decaying wood can be highly variable. The general pattern is an increase of bacteria with progressive decay, but we also identified several fungi that were apparently able to exclude bacteria from their woody territory. We established a bacterial collection which is highly representative for decaying wood with typical wood-inhabiting taxa: Xanthomonadaceae, Acetobacteraceae, Caulobacteraceae, Methylovirgula, Sphingomonas, Burkholderia and Granulicella. In vitro antagonistic activity against other bacteria and fungi was evaluated. In contrast to our hypothesis, we found surprisingly low antagonistic activity against bacteria (<2% of isolates), while antagonism against fungi was more prevalent. These results may point at a prominent role of mycophagy (growth at the expense of living fungi) among wood-inhabiting bacteria.

microbiology↗