Bacterial chitin hydrolysis in two lakes with contrasting trophic statuses

Macrophyte Restoration Promotes Lake Microbial Carbon Pump to Enhance Aquatic Carbon Sequestration

Macrophyte-based lake restoration has successfully transitioned lakes from turbid conditions dominated by phytoplankton to a more natural, clear state; however, its impact on microbial carbon pump-mediated dissolved organic carbon (DOM) storage and greenhouse gas (GHG) emissions in the aquatic ecosystem remains largely unexplored. Through a year-long field study, we conducted a comparative analysis of two alternative habitats within the same lake-restored and unrestored areas. Results demonstrated that restoration not only substantially decreases nutrient levels and algal blooms-evidenced by over 50% reductions in nitrogen, phosphorus, and chlorophyll a-but also significantly increases the accumulation of recalcitrant DOM. This is characterized by rises of 9.52% in highly unsaturated compounds, 8.68% in carboxyl-rich alicyclic molecules, 37.54% polycyclic condensed aromatics and polyphenols, and 20.21% in SUVA254. Additionallly, key microbial taxa with potent carbon pump functions-primarily Gammaproteobacteria, Alphaproteobacteria, and Actinobacteria-are enriched in restored areas. Structural equation modeling (SEM) further elucidated the complex interrelationships within more pristine lake ecosystems: macrophytes and elevated dissolved oxygen (DO) concentrations enhance carbon sequestration via microbial carbon pump pathways, while the restoration significantly mitigates methane emissions caused by eutrophication. These findings highlight an extra function of aquatic macrophyte restoration, offering valuable insights into microbial processes for future restoration efforts aimed at promoting sustainable aquatic ecosystems and mitigating global warming.

Tire wear particles enhance horizontal gene transfer of antibiotic resistance genes in aquatic ecosystems

Microplastics (MPs) have introduced new surfaces for biofilm development and gene exchange among bacteria. We investigated Tire Wear Particles (TWPs) for their involvement in horizontal gene transfer (HGT), particularly in relation to associated metals in the matrices of TWPs. We employed red-fluorescently tagged E. coli strain as a donor with green-fluorescently tagged, broad-host-range plasmid pKJK5, resistant to trimethoprim. As a recipient, we utilized Pseudomonas sp. and a natural lake microbial community. HGT activity on TWPs was determined and compared with that on polystyrene (PS) (with and without metals), and chitosan, which was used as a natural surface. Exposure to TWPs significantly enhanced HGT frequency of antibiotic resistance gene (ARG) from donor to recipient compared to PS and chitosan, and metals of TWPs further promoted HGT. HGT frequency on TWPs with Pseudomonas sp. was found to be 10-3 at 30 °C. in the lake community, it was similarly high already at 25 °C suggesting a higher permissiveness of the natural microbial community towards ARG at lower temperatures. This study sheds light on the potential impact of TWPs in promoting HGT, forming the basis for health risk assessments of TWPs and more generally of MP pollution in various aquatic ecosystems.

Removal of primary nutrient degraders reduces growth of soil microbial communities with genomic redundancy

Introduction

Understanding how microorganisms within a soil community interact to support collective respiration and growth remains challenging. Here, we used a model substrate, chitin, and a synthetic Model Soil Consortium (MSC-2) to investigate how individual members of a microbial community contribute to decomposition and community growth. While MSC-2 can grow using chitin as the sole carbon source, we do not yet know how the growth kinetics or final biomass yields of MSC-2 vary when certain chitin degraders, or other important members, are absent.

Methods

To characterize specific roles within this synthetic community, we carried out experiments leaving out members of MSC-2 and measuring biomass yields and CO2 production. We chose two members to iteratively leave out (referred to by genus name): Streptomyces, as it is predicted via gene expression analysis to be a major chitin degrader in the community, and Rhodococcus as it is predicted via species co-abundance analysis to interact with several other members.

Results

Our results showed that when MSC-2 lacked Streptomyces, growth and respiration of the community was severely reduced. Removal of either Streptomyces or Rhodococcus led to major changes in abundance for several other species, pointing to a comprehensive shifting of the microbial community when important members are removed, as well as alterations in the metabolic profile, especially when Streptomyces was lacking. These results show that when keystone, chitin degrading members are removed, other members, even those with the potential to degrade chitin, do not fill the same metabolic niche to promote community growth. In addition, highly connected members may be removed with similar or even increased levels of growth and respiration.

Discussion

Our findings are critical to a better understanding of soil microbiology, specifically in how communities maintain activity when biotic or abiotic factors lead to changes in biodiversity in soil systems.

Reversible Metal Ion/Complex Binding to Chitin Controlled by Ligand, Redox, and Photochemical Reactions and Active Movement of Chitin on Aquatic Arthropods

There is strong adsorption of metal ions and their complexes to chitin, which depends on both the oxidation and complexation states of many of the said elements (whereas others display chemical reactions detectable via electrochemical methods while being retained by chitin); thus, ad- and desorption at ambient water concentrations (often in the nMol/L range) are controlled by the presence and photochemical properties (concerning Eu and probably U and Ag) of mainly biogenic organic matter (both DOC and POC, and DON). With chitin forming the outer hull of mobile organisms (animals), this biopolymer is expected to take part in metal distribution in aquatic (limnetic and riverine) ecosystems. Having studied the attachment of many different elements to both crayfish and grafted (marine shrimp) chitin, with the highest accumulations observed in Bi, V, Ni, and LREEs, one should consider secondary biochemical transformations which take place at different water and sediment levels. After chitin had been embedded into sediment, methanogenesis (which requires Ni), Bi, and Sb biomethylations and photodesorption in the illuminated water column will occur if there are appropriate organics, causing the vertical separation of Eu from other REEs, at least during the daytime. Eutrophication will enhance both the production and especially the photooxidation rates of organics in water because phosphorylated sugars and lipids are formed quantitatively within min P, which enter water and undergo Eu-mediated photooxidation much more readily. Another biopolymer, gelatin, acts as an inert matrix-enhancing organic photooxidation product via Eu, producing chemical waves, indicating autocatalysis upon light impact. From the redox-related photodesorption of metal analytes from chitin, both sensors and devices for (light-assisted) electrochemical energy conversion are being developed by our workgroup. The electrochemical determination of adsorption thermodynamics on chitin is thus directly linked to its applications in environmental monitoring and technology.

Microbial Succession of Anaerobic Chitin Degradation in Freshwater Sediments

Chitin is the most abundant biopolymer in aquatic environments, with a direct impact on the carbon and nitrogen cycles. Despite its massive production as a structural element of crustaceans, insects, or algae, it does not accumulate in sediments. Little is known about its turnover in predominantly anoxic freshwater sediments and the responsible microorganisms. We proved that chitin is readily degraded under anoxic conditions and linked this to a succession of the members of the responsible microbial community over a 43-day period. While Fibrobacteres and Firmicutes members were driving the early and late phases of chitin degradation, respectively, a more diverse community was involved in chitin degradation in the intermediate phase. Entirely different microorganisms responded toward the chitin monomer N-acetylglucosamine, which underscores that soluble monomers are poor and misleading substrates to study polymer-utilizing microorganisms. Our study provides quantitative insights into the microbial ecology driving anaerobic chitin degradation in freshwater sediments.

Chitin is massively produced by freshwater plankton species as a structural element of their exoskeleton or cell wall. At the same time, chitin does not accumulate in the predominantly anoxic sediments, underlining its importance as carbon and nitrogen sources for sedimentary microorganisms. We studied chitin degradation in littoral sediment of Lake Constance, Central Europe’s third largest lake. Turnover of the chitin analog methyl-umbelliferyl-N,N-diacetylchitobioside (MUF-DC) was highest in the upper oxic sediment layer, with 5.4 nmol MUF-DC h⁻¹ (g sediment [dry weight])⁻¹. In the underlying anoxic sediment layers, chitin hydrolysis decreased with depth from 1.1 to 0.08 nmol MUF-DC h⁻¹ (g sediment [dry weight])⁻¹. Bacteria involved in chitin degradation were identified by 16S rRNA (gene) amplicon sequencing of anoxic microcosms incubated in the presence of chitin compared to microcosms amended either with N-acetylglucosamine as the monomer of chitin or no substrate. Chitin degradation was driven by a succession of bacteria responding specifically to chitin only. The early phase (0 to 9 days) was dominated by Chitinivibrio spp. (Fibrobacteres). The intermediate phase (9 to 21 days) was characterized by a higher diversity of chitin responders, including, besides Chitinivibrio spp., also members of the phyla Bacteroidetes, Proteobacteria, Spirochaetes, and Chloroflexi. In the late phase (21 to 43 days), the Chitinivibrio populations broke down with a parallel strong increase of Ruminiclostridium spp. (formerly Clostridium cluster III, Firmicutes), which became the dominating chitin responders. Our study provides quantitative insights into anaerobic chitin degradation in lake sediments and linked this to a model of microbial succession associated with this activity.

IMPORTANCE Chitin is the most abundant biopolymer in aquatic environments, with a direct impact on the carbon and nitrogen cycles. Despite its massive production as a structural element of crustaceans, insects, or algae, it does not accumulate in sediments. Little is known about its turnover in predominantly anoxic freshwater sediments and the responsible microorganisms. We proved that chitin is readily degraded under anoxic conditions and linked this to a succession of the members of the responsible microbial community over a 43-day period. While Fibrobacteres and Firmicutes members were driving the early and late phases of chitin degradation, respectively, a more diverse community was involved in chitin degradation in the intermediate phase. Entirely different microorganisms responded toward the chitin monomer N-acetylglucosamine, which underscores that soluble monomers are poor and misleading substrates to study polymer-utilizing microorganisms. Our study provides quantitative insights into the microbial ecology driving anaerobic chitin degradation in freshwater sediments.

Understanding microbial community dynamics to improve optimal microbiome selection

BACKGROUND

Artificial selection of microbial communities that perform better at a desired process has seduced scientists for over a decade, but the method has not been systematically optimised nor the mechanisms behind its success, or failure, determined. Microbial communities are highly dynamic and, hence, go through distinct and rapid stages of community succession, but the consequent effect this may have on artificially selected communities is unknown.

RESULTS

Using chitin as a case study, we successfully selected for microbial communities with enhanced chitinase activities but found that continuous optimisation of incubation times between selective transfers was of utmost importance. The analysis of the community composition over the entire selection process revealed fundamental aspects in microbial ecology: when incubation times between transfers were optimal, the system was dominated by Gammaproteobacteria (i.e. main bearers of chitinase enzymes and drivers of chitin degradation), before being succeeded by cheating, cross-feeding and grazing organisms.

CONCLUSIONS

The selection of microbiomes to enhance a desired process is widely used, though the success of artificially selecting microbial communities appears to require optimal incubation times in order to avoid the loss of the desired trait as a consequence of an inevitable community succession. A comprehensive understanding of microbial community dynamics will improve the success of future community selection studies.

Identification of a novel chitinase from Aeromonas hydrophila AH-1N for the degradation of chitin within fungal mycelium

Defined organic waste products are ideal and sustainable secondary feedstocks for production organisms in microbial biotechnology. Chitin from mycelia of fungal fermentation processes represents a homogeneous and constantly available waste product that can, however, not be utilised by typical bacterial production strains. Therefore, enzymes that degrade chitin within fungal mycelia have to be identified and expressed in production organisms. In this study, chitin-degrading bacteria were enriched and isolated from lake water with mycelia of Aspergillus tubingensis as sole organic growth substrate. This approach yielded solely strains of Aeromonas hydrophila. Comparison of the isolated strains with other A. hydrophila strains regarding their chitinolytic activities on fungal mycelia identified strain AH-1N as the best enzyme producer. From this strain, a chitinase (EC:3.2.1.14) was identified by peptide mass fingerprinting. Heterologous expression of the respective gene combined with mass spectrometry showed that the purified enzyme was capable of releasing chitobiose from fungal mycelia with a higher yield than a well-described chitinase from Serratia marcescens. Expression of the newly identified chitinase in biotechnological production strains could be the first step for making fungal mycelium accessible as a secondary feedstock. Additionally, the enrichment strategy proved to be feasible for identifying strains able to degrade fungal chitin.

Microplastics increase impact of treated wastewater on freshwater microbial community

Plastic pollution is a major global concern with several million microplastic particles entering every day freshwater ecosystems via wastewater discharge. Microplastic particles stimulate biofilm formation (plastisphere) throughout the water column and have the potential to affect microbial community structure if they accumulate in pelagic waters, especially enhancing the proliferation of biohazardous bacteria. To test this scenario, we simulated the inflow of treated wastewater into a temperate lake using a continuous culture system with a gradient of concentration of microplastic particles. We followed the effect of microplastics on the microbial community structure and on the occurrence of integrase 1 (int1), a marker associated with mobile genetic elements known as a proxy for anthropogenic effects on the spread of antimicrobial resistance genes. The abundance of int1 increased in the plastisphere with increasing microplastic particle concentration, but not in the water surrounding the microplastic particles. Likewise, the microbial community on microplastic was more similar to the original wastewater community with increasing microplastic concentrations. Our results show that microplastic particles indeed promote persistence of typical indicators of microbial anthropogenic pollution in natural waters, and substantiate that their removal from treated wastewater should be prioritised.

The effects of arbuscular mycorrhizal fungi and essential oil on soil microbial community and N-related enzymes during the fungal early colonization phase

The arbuscular mycorrhizal fungi (AMF) and the essential oils are both agents of sustainable agriculture, and their independent effects on the community of free-living soil microbes have been explored. In a tomato pot experiment, conducted in a sandy loam mixture, we examined the independent and joint effects of inoculation with the fungus Rhizophagous irregularis and the addition of Mentha spicata essential oil on the structure of the soil microbial community and the activity of soil enzymes involved in the N-cycle, during the pre-symbiosis phase. Plants were grown for 60 days and were inoculated with R. irregularis. Then pots were treated with essential oil (OIL) weekly for a period of a month. Two experimental series were run. The first targeted to examine the effect of inoculation on the microbial community structure by the phospholipid fatty acids analysis (PLFAs), and enzyme activity, and the second to examine the effects of inoculation and essential oil addition on the same variables, under the hypothesis that the joint effect of the two agents would be synergistic, resulting in higher microbial biomass compared to values recorded in singly treated pots. In the AMF pots, N-degrading enzyme activity was dominated by the activity of urease while in the non-inoculated ones by the activities of arylamidase and glutaminase. Higher microbial biomass was found in singly-treated pots (137 and 174% higher in AMF and OIL pots, respectively) compared with pots subjected to both treatments. In these latter pots, higher activity of asparaginase (202 and 162% higher compared to AMF and OIL pots, respectively) and glutaminase (288 and 233% higher compared to AMF and OIL pots, respectively) was found compared to singly-treated ones. Soil microbial biomasses and enzyme activity were negatively associated across all treatments. Moreover, different community composition was detected in pots only inoculated and pots treated only with oil. We concluded that the two treatments produced diverging than synergistic effects on the microbial community composition whereas their joint effect on the activity of asparaginase and glutaminase were synergistic.

Bacterial epibionts of Daphnia: a potential route for the transfer of dissolved organic carbon in freshwater food webs

The identification of interacting species and elucidation of their mode of interaction may be crucial to understand ecosystem-level processes. We analysed the activity and identity of bacterial epibionts in cultures of Daphnia galeata and of natural daphnid populations. Epibiotic bacteria incorporated considerable amounts of dissolved organic carbon (DOC), as estimated via uptake of tritiated leucine: three times more tracer was consumed by microbes on a single Daphnia than in 1 ml of lake water. However, there was virtually no incorporation if daphnids were anaesthetised, suggesting that their filtration activity was essential for this process. Microbial DOC uptake could predominantly be assigned to microbes that were located on the filter combs of daphnids, where the passage of water would ensure a continuously high DOC supply. Most of these bacteria were Betaproteobacteria from the genus Limnohabitans. Specifically, we identified a monophyletic cluster harbouring Limnohabitans planktonicus that encompassed sequence types from D. galeata cultures, from the gut of Daphnia magna and from daphnids of Lake Zurich. Our results suggest that the epibiotic growth of bacteria related to Limnohabitans on Daphnia spp. may be a widespread and rather common phenomenon. Moreover, most of the observed DOC flux to Daphnia in fact does not seem to be associated with the crustacean biomass itself but with its epibiotic microflora. The unexplored physical association of daphnids with heterotrophic bacteria may have considerable implications for our understanding of carbon transfer in freshwater food webs, that is, a trophic 'shortcut' between microbial DOC uptake and predation by fish.

Bacterial chitin degradation-mechanisms and ecophysiological strategies

Chitin is one the most abundant polymers in nature and interacts with both carbon and nitrogen cycles. Processes controlling chitin degradation are summarized in reviews published some 20 years ago, but the recent use of culture-independent molecular methods has led to a revised understanding of the ecology and biochemistry of this process and the organisms involved. This review summarizes different mechanisms and the principal steps involved in chitin degradation at a molecular level while also discussing the coupling of community composition to measured chitin hydrolysis activities and substrate uptake. Ecological consequences are then highlighted and discussed with a focus on the cross feeding associated with the different habitats that arise because of the need for extracellular hydrolysis of the chitin polymer prior to metabolic use. Principal environmental drivers of chitin degradation are identified which are likely to influence both community composition of chitin degrading bacteria and measured chitin hydrolysis activities.

Grazing resistant freshwater bacteria profit from chitin and cell-wall-derived organic carbon

The rise of grazing resistant planktonic bacteria in freshwater lakes during vernal phytoplankton blooms is favoured by predation of heterotrophic nanoflagellates (HNF). The spring period is also characterized by increased availability of organic carbon species that are in parts derived from cellular debris generated during bacterivory or viral lysis, such as peptidoglycan, chitin and their subunit N-acetylglucosamine (NAG). We tested the hypothesis that two dominant grazing resistant bacterial taxa, the ac1 tribe of Actinobacteria (ac1) and filamentous bacteria from the LD2 lineage (Saprospiraceae), profit from such carbon sources during periods of intense HNF predation. The abundances of ac1 and LD2 rose in parallel with HNF, and disproportionally high fractions of cells from both lineages were involved in NAG uptake. Members of ac1 and LD2 were significantly more enriched after NAG addition to lake water. However, highest growth rates of both bacterial lineages were found on chitin and peptidoglycan. Moreover, the direct or indirect transfer of organic carbon from peptidoglycan to LD2 filaments could be demonstrated. We thus provide evidence that these taxa may benefit twofold from protistan predation: by removal of their competitors, and by specific physiological adaptations to utilize carbon sources that are released during grazing or viral lysis.

Simple absolute quantification method correcting for quantitative PCR efficiency variations for microbial community samples

Real-time quantitative PCR (qPCR) is a widely used technique in microbial community analysis, allowing the quantification of the number of target genes in a community sample. Currently, the standard-curve (SC) method of absolute quantification is widely employed for these kinds of analysis. However, the SC method assumes that the amplification efficiency (E) is the same for both the standard and the sample target template. We analyzed 19 bacterial strains and nine environmental samples in qPCR assays, targeting the nifH and 16S rRNA genes. The E values of the qPCRs differed significantly, depending on the template. This has major implications for the quantification. If the sample and standard differ in their E values, quantification errors of up to orders of magnitude are possible. To address this problem, we propose and test the one-point calibration (OPC) method for absolute quantification. The OPC method corrects for differences in E and was derived from the ΔΔC(T) method with correction for E, which is commonly used for relative quantification in gene expression studies. The SC and OPC methods were compared by quantifying artificial template mixtures from Geobacter sulfurreducens (DSM 12127) and Nostoc commune (Culture Collection of Algae and Protozoa [CCAP] 1453/33), which differ in their E values. While the SC method deviated from the expected nifH gene copy number by 3- to 5-fold, the OPC method quantified the template mixtures with high accuracy. Moreover, analyzing environmental samples, we show that even small differences in E between the standard and the sample can cause significant differences between the copy numbers calculated by the SC and the OPC methods.