Anoxic chlorophyll maximum enhances local organic matter remineralization and nitrogen loss in Lake Tanganyika

Isotopic signatures induced by upwelling reveal regional fish stocks in Lake Tanganyika

Lake Tanganyika's pelagic fish sustain the second largest inland fishery in Africa and are under pressure from heavy fishing and global warming related increases in stratification. The strength of water column stratification varies regionally, with a more stratified north and an upwelling-driven, biologically more productive south. Only little is known about whether such regional hydrodynamic regimes induce ecological or genetic differences among populations of highly mobile, pelagic fish inhabiting these different areas. Here, we examine whether the regional contrasts leave distinct isotopic imprints in the pelagic fish of Lake Tanganyika, which may reveal differences in diet or lipid content. We conducted two lake-wide campaigns during different seasons and collected physical, nutrient, chlorophyll, phytoplankton and zooplankton data. Additionally, we analyzed the pelagic fish-the clupeids Stolothrissa tanganicae, Limnothrissa miodon and four Lates species-for their isotopic and elemental carbon (C) and nitrogen (N) compositions. The δ13C values were significantly higher in the productive south after the upwelling/mixing period across all trophic levels, implying that the fish have regional foraging grounds, and thus record these latitudinal isotope gradients. By combining our isotope data with previous genetic results showing little geographic structure, we demonstrate that the fish reside in a region for a season or longer. Between specimens from the north and south we found no strong evidence for varying trophic levels or lipid contents, based on their bulk δ15N and C:N ratios. We suggest that the development of regional trophic or physiological differences may be inhibited by the lake-wide gene flow on the long term. Overall, our findings show that the pelagic fish species, despite not showing evidence for genetic structure at the basin scale, form regional stocks at the seasonal timescales. This implies that sustainable management strategies may consider adopting regional fishing quotas.

Hydrodynamic regimes modulate nitrogen fixation and the mode of diazotrophy in Lake Tanganyika

The factors that govern the geographical distribution of nitrogen fixation are fundamental to providing accurate nitrogen budgets in aquatic environments. Model-based insights have demonstrated that regional hydrodynamics strongly impact nitrogen fixation. However, the mechanisms establishing this physical-biological coupling have yet to be constrained in field surveys. Here, we examine the distribution of nitrogen fixation in Lake Tanganyika - a model system with well-defined hydrodynamic regimes. We report that nitrogen fixation is five times higher under stratified than under upwelling conditions. Under stratified conditions, the limited resupply of inorganic nitrogen to surface waters, combined with greater light penetration, promotes the activity of bloom-forming photoautotrophic diazotrophs. In contrast, upwelling conditions support predominantly heterotrophic diazotrophs, which are uniquely suited to chemotactic foraging in a more dynamic nutrient landscape. We suggest that these hydrodynamic regimes (stratification versus mixing) play an important role in governing both the rates and the mode of nitrogen fixation.

Phytoplankton pigment dynamics in marine lake fluctuating between stratified and holomictic euxinic conditions

Biomass dynamics in the marine lake are strongly dependent on seasonal variability in vertical stratification, indicating rapid adaptation of phytoplankton to short-term changes in the water column. A small marine lake (Rogoznica Lake, Croatia), which fluctuates between stably stratified and holomictic euxinic conditions, was used as a model to study the phytoplankton responses to environmental perturbations, in particular the anoxic stress, caused by periodic holomixia. The epilimnion showed significant temporal and vertical variability with a chlorophyll a subsurface maximum with the highest biomass near the chemocline. Fucoxanthin-containing biomass (diatoms) dominated in the epilimnion in colder seasons and was first to recover after holomictic euxinic events. The shift towards the smaller groups prevailed during highly stratified water column conditions in warmer seasons. Results for the hypolimnion were more enigmatic, with high concentrations of alloxanthin, zeaxanthin, and violaxanthin indicating the presence of a viable small-size mixotrophic community under extreme conditions.

Nitrite accumulation and anammox bacterial niche partitioning in Arctic Mid-Ocean Ridge sediments

By consuming ammonium and nitrite, anammox bacteria form an important functional guild in nitrogen cycling in many environments, including marine sediments. However, their distribution and impact on the important substrate nitrite has not been well characterized. Here we combined biogeochemical, microbiological, and genomic approaches to study anammox bacteria and other nitrogen cycling groups in two sediment cores retrieved from the Arctic Mid-Ocean Ridge (AMOR). We observed nitrite accumulation in these cores, a phenomenon also recorded at 28 other marine sediment sites and in analogous aquatic environments. The nitrite maximum coincides with reduced abundance of anammox bacteria. Anammox bacterial abundances were at least one order of magnitude higher than those of nitrite reducers and the anammox abundance maxima were detected in the layers above and below the nitrite maximum. Nitrite accumulation in the two AMOR cores co-occurs with a niche partitioning between two anammox bacterial families (Candidatus Bathyanammoxibiaceae and Candidatus Scalinduaceae), likely dependent on ammonium availability. Through reconstructing and comparing the dominant anammox genomes (Ca. Bathyanammoxibius amoris and Ca. Scalindua sediminis), we revealed that Ca. B. amoris has fewer high-affinity ammonium transporters than Ca. S. sediminis and lacks the capacity to access alternative substrates and/or energy sources such as urea and cyanate. These features may restrict Ca. Bathyanammoxibiaceae to conditions of higher ammonium concentrations. These findings improve our understanding about nitrogen cycling in marine sediments by revealing coincident nitrite accumulation and niche partitioning of anammox bacteria.

Transition of source/sink processes and fate of ammonium in groundwater along with redox gradients

Ammonium (NH₄⁺) retention/removal processes in groundwater are of great interest because of the continuous increase in nitrogenous compound loading due to anthropogenic activities. However, the transition of multiple co-occurring transformation processes that determine the fate of NH₄⁺ in groundwater along a redox gradient remains underexplored. We selected a high nitrogen (N) groundwater system in the western Hetao Basin, China, to identify and quantify NH₄⁺ source and sink processes, including mineralization, dissimilatory nitrate reduction to ammonium (DNRA), nitrification, and anammox, to better understand the dynamics of NH₄⁺. Based on redox-sensitive parameters, that is, the oxidation-reduction potential (ORP) and NH₄⁺ and nitrate (NO₃^-) contents, etc., the groundwater system was classified into three zones from upstream to downstream: zone I (oxidizing), zone II (moderately reducing), and zone III (strongly reducing). Using the ¹⁵N tracing technique, we found that NH₄⁺ was mainly produced by mineralization while < 2% was produced by DNRA throughout the study area. Mineralization increased downstream because the supply of biodegradable N-containing compounds was augmented, which created a strong redox gradient to host a serial reaction chain. In zone I, NH₄⁺ was mainly transferred to NO₃^- via nitrification, whereas in zones II and III, NH₄⁺ was mainly transferred to N₂ via anammox. The average NH₄⁺ production/consumption ratios (P/C) in zones I, II, and III were 0.7, 6.9, and 51.1, respectively. Obviously, the NH₄⁺ purification ability can only exceed the supply under aerobic conditions, thus suggesting that NH₄⁺ will accumulate without limitation and be retained in strongly reducing groundwater. The situation of NH₄⁺ accumulation would deteriorate over space and time in groundwater as human activities increase without an additional artificial supply of oxidants. The results provide mechanistic insights for quantitatively comprehending the dynamics and fate of NH₄⁺ in groundwater, shedding light on groundwater NH₄⁺ mitigation techniques.

Changes of endophytic microbial community in Rhododendron simsii roots under heat stress and its correlation with leaf physiological indicators

Introduction

The response mechanism of Rhododendron simsii and its endophytic microorganism to heat stress is still unclear.

Methods

The light incubator was used to set the temperature gradients, and the control (CK) was (day/night: 14/10 h) 25/22°C, the moderate-heat-stress (MHS) was 35/30°C and the high-heat-stress (HHS) was 40/35°C.

Results

Compared with CK, MHS significantly increased the contents of malondialdehyde, hydrogen peroxide, proline, and soluble sugar, as well as the activities of catalase and peroxidase in leaf, while HHS increased the activities of ascorbate peroxidase, and decreased chlorophyll content. Compared with CK, MHS reduced soil available nitrogen (N) content. Both heat stress changed the endophytic microbial community structure in roots. MHS enriched Pezicula and Paracoccus, while HHS significantly enriched Acidothermus and Haliangium. The abundance of Pezicula positively correlated with the contents of chlorophyll a and proline in leaf, and negatively correlated with soil ammonium N content. The abundance of Pezicula and Haliangium positively correlated with soluble sugar and malondialdehyde contents, respectively.

Conclusions

Our results suggest that root endophytic microorganisms play an important role in helping Rhododendron resisting heat stress, mainly by regulating soil N content and plant physiological characteristics.

Sediment organic matter properties facilitate understanding nitrogen transformation potentials in East African lakes

East African lakes include the most productive and alkaline lake group in the world. Yet, they generally receive fewer nutrient inputs than the densely populated subtropical and temperate lakes in the northern hemisphere. In these lakes with insufficient supplies of inorganic nitrogen, the mineralization of benthic organic matter can play an important role in driving the nutrient cycle and nitrogen loss. Using a suite of stable ¹⁵N isotope dilution and tracer techniques, we examined five main processes of the sediment nitrogen cycle in 16 lakes and reservoirs of Tanzania and Kenya, East Africa: gross nitrogen mineralization, ammonium immobilization, dissimilatory nitrate reduction to ammonium (DNRA), and the dinitrogen (N₂) production via denitrification and anaerobic ammonium oxidation (anammox). Gross nitrogen mineralization and ammonium immobilization showed the maximum values of 9.84 and 12.39 μmol N kg^-1 h^-1, respectively. Potential DNRA rates ranged from 0.22 to 8.15 μmol N kg^-1 h^-1 and accounted for 10 %-74 % (average 25 %) of the total dissimilatory nitrate reduction. Potential nitrate reduction rates in most lakes were dominated by denitrification with a contribution of 26 %-85 % and a mean of 65 %. We further found that the sediment nitrogen transformations were driven mainly by benthic organic matter properties and water column phosphate concentrations, reflecting microbial metabolic responses to the changing carbon and nutrients availability. For instance, autochthonous production of protein-like organic matter attributed to active sediment nitrogen mineralization, DNRA, and denitrification. In contrast, the high degree of humification caused by the inputs of terrestrial humic-like substances slowed down the sediment nitrogen transformations. The contribution of DNRA to total dissimilatory nitrate reduction was significantly positively correlated to sediment C: N ratios. These results indicate that predictions of sediment N supply and loss in East African lakes can be improved by incorporating sediment organic matter properties.

Microbial Nitrogen Transformation Potential in Sediments of Two Contrasting Lakes Is Spatially Structured but Seasonally Stable

The nitrogen (N) cycle is of global importance, as N is an essential element and a limiting nutrient in terrestrial and aquatic ecosystems. Excessive anthropogenic N fertilizer usage threatens sensitive downstream aquatic ecosystems. Although freshwater lake sediments remove N through various microbially mediated processes, few studies have investigated the microbial communities involved. In an integrated biogeochemical and microbiological study on a eutrophic and oligotrophic lake, we estimated N removal rates from pore water concentration gradients in sediments. Simultaneously, the abundance of different microbial N transformation genes was investigated using metagenomics on a seasonal and spatial scale. We observed that contrasting nutrient concentrations in sediments were associated with distinct microbial community compositions and significant differences in abundances of various N transformation genes. For both characteristics, we observed a more pronounced spatial than seasonal variability within each lake. The eutrophic Lake Baldegg showed a higher denitrification potential with higher nosZ gene (N₂O reductase) abundances and higher nirS:nirK (nitrite reductase) ratios, indicating a greater capacity for complete denitrification. Correspondingly, this lake had a higher N removal efficiency. The oligotrophic Lake Sarnen, in contrast, had a higher potential for nitrification. Specifically, it harbored a high abundance of Nitrospira, including some with the potential for comammox. Our results demonstrate that knowledge of the genomic N transformation potential is important for interpreting N process rates and understanding how the lacustrine sedimentary N cycle responds to variations in trophic conditions.

IMPORTANCE Anthropogenic nitrogen (N) inputs can lead to eutrophication in surface waters, especially in N-limited coastal ecosystems. Lakes effectively remove reactive N by transforming it to N₂ through microbial denitrification or anammox. The rates and distributions of these microbial processes are affected by factors such as the amount and quality of settling organic material and nitrate concentrations. However, the microbial communities mediating these N transformation processes in freshwater lake sediments remain largely unknown. We provide the first seasonally and spatially resolved metagenomic analysis of the N cycle in sediments of two lakes with different trophic states. We show that lakes with different trophic states select for distinct communities of N-cycling microorganisms with contrasting functional potentials for N transformation.

Diversity of endophytic bacteria in wild rice (Oryza meridionalis) and potential for promoting plant growth and degrading phthalates

Phthalates (PAEs) accumulated in agricultural soils and rice have increased human exposure risks. Microbial degradation could efficiently reduce the residue of organic pollutants in soil and crop plants. Here, we hypothesized that endophytic bacteria from wild rice have the potential for degradation of PAEs and plant growth promoting. The endophytic bacterial community and functional diversity in wild rice (Oryza meridionalis) were analyzed for the first time, and the potential for PAE degradation and plant growth promoting by endophytes were investigated. The results of Illumina high-throughput sequencing revealed that abundant endophytes inhabited in wild rice with Proteobacteria, Bacteroidetes, Firmicutes and Actinobacteria being the dominant phyla. Endophytic bacterial diversity and complexity were confirmed by isolation and clustering of isolates. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that endophytes exerted diverse functions such as plant growth promoting, xenobiotics biodegradation, pollution remediation and bacterial chemotaxis. Pure culture experiment showed that 30 isolated endophytic strains exhibited in vitro plant growth promoting activities, and rice plants inoculated with these strains confirmed their growth promoting abilities. Some endophytic strains were capable of efficiently degrading PAEs, with the highest removal percentage of di-n-butyl phthalate (DBP) up to 96.1% by Bacillus amyloliquefaciens strain L381 within 5 days. Synthetic community F and strain L381 rapidly removed DBP from soil (removing 91.0%-99.2% within 10 d and from rice plant slurry (removing 93.4%-99.2% within 5 d). These results confirmed the hypothesis and demonstrated the diversity of endophytic bacteria in wild rice with diverse functions, especially for plant growth promoting and removing PAEs. These multifunctional endophytic bacteria provided good alternatives to reduce PAE accumulation in crops and increase yield.