Microbial use of low molecular weight DOM in filtered and unfiltered freshwater: Role of ultra-small microorganisms and implications for water quality monitoring

Anthropogenic original DOM is a critical factor affecting LNA bacterial community assembly

We investigated the geographical and environmental distance-decay relationships for both of the two bacteria in the Haihe River, Tianjin, China. HNA bacteria exhibited a stronger geographical variation-dependent pattern while LNA bacteria exhibited a stronger environmental variation-dependent pattern. Variance partition analysis (VPA), Mantel test, and partial mantel test validated the discrepant impacts of geographical distance and environmental factors on their two communities. The heterogeneous selection dominated community assembly of LNA bacteria demonstrates their greater sensitivity to environmental conditions. As the deterministic environmental factor, anthropogenic original dissolved organic matter (DOM) functions exclusively on LNA bacteria, and it is the critical factor leading to the discrepant biogeographical patterns of LNA and HNA bacteria. LNA bacteria interact with HNA bacteria and mediate the DOM driving total bacteria assembly. The LNA keystone taxa, Pseudomonas, Rheinheimera, Candidatus Aquiluna, and hgcl clade are capable to compete with HNA bacteria for anthropogenic original DOM, and are potential indicators of anthropogenic pollution. Our research reveals the non-negligible effect of the LNA bacteria in regulating the ecological response of total bacteria.

Interaction among biofilter microbiome, fecal metabolome and water quality and regulation of sewage discharge in the recirculating aquaculture system of Apostichopus japonicus

With the aggravation of environmental pollution caused by traditional culture of Apostichopus japonicus, the concept of A. japonicus recirculating aquaculture system (RAS) came into being. To plan the sewage discharge time reasonably, we explored the temporal variation of water quality, biofilter microbe and fecal metabolome in RAS and relevant mechanism. The results showed that monitored water quality in RAS were within the safe living range of A. japonicus. Proteobacteria and Desulfobacterota were dominant bacteria in biofilter. The RDA results and correlation heatmap showed that NH₄-N and NO₂-N significantly affected the microbial community composition. The expression pattern of fecal metabolites changed with the passage of time after feeding. And ROC curve analysis and VIP bar chart showed that there were inter group biomarkers with predictive performance, which could help to remind timely sewage discharge. Topological analysis of KEGG pathway enrichment showed that metabolic pathways such as alanine, aspartate and glutamate metabolism changed significantly after feeding (P < 0.01). Additionally, the correlation analysis results showed that biofilter microbe and fecal metabolites were related to water quality (P < 0.05). Combined with the above research results, this study concluded that the RAS could discharge sewage 25-30 h after feeding. These findings were of direct significance to the management of RAS environment and the protection of A. japonicus healthy growth.

Regional-scale investigation of the molecular weight distribution and metal-binding behavior of dissolved organic matter from a shallow macrophytic lake using multispectral techniques

In this work, based on excitation-emission matrix spectroscopy combined with parallel factor analysis (EEM-FARAFAC) and two-dimensional correlation analysis of synchronous fluorescence spectroscopy, Fourier transform infrared spectroscopy, and combination of two spectra (2D-SF-COS, 2D-FTIR-COS, and Hetero-2D-COS), the characteristics and metal-binding behaviors of DOM in Dongping Lake were explored for molecular weight (MW), fluorescence components, and functional groups. The results showed that the entire lake was governed by protein-like materials with low MW(< 1 kDa). The complexation occurred preferentially in protein-like materials for bulk DOM after adding copper (Cu²⁺) and lead (Pb²⁺), which were changed by fractionation for MW. The active points were aliphatic C－OH for DOM-Cu and phenol －OH or polysaccharide for DOM-Pb from 2D-FTIR-COS. The protein-like components possessed higher LogK than humic-like component during binding to Cu²⁺ or Pb²⁺. Moreover, the complexing affinities of DOM-Cu (LogK_Cu: 3.26 ± 0.87-4.04 ± 0.49) were higher than those of DOM-Pb (LogK_Pb: 2.66 ± 0.52-3.78 ± 0.36). On a spatial scale, high LogK_Cu and LogK_Pb were found in the center and entrance of the lake, respectively. Humic-like component C2 in the LMW fraction possessed a stronger binding capacity with Cu²⁺. This study affords new insights into the migration and conversion of HMs in lakes.

Sampling, storage and laboratory approaches for dissolved organic matter characterisation in freshwaters: Moving from nutrient fraction to molecular-scale characterisation

Recent research has highlighted the importance of dissolved organic matter (DOM) for ecosystem function and because of this paradigm shift, it has become crucial to not only quantify its contribution to river nutrient loads but also to characterise its composition. There has been a significant research effort utilising optical methods, such as fluorescence and UV-Vis spectrophotometry, in order to start exploring DOM character. However, these methods still lack the granularity to understand the chemical composition at the molecular level, which is vital to properly understanding its functional role in freshwater ecosystems. As a direct result, there has been a shift towards including molecular-scale analyses to investigate the in-stream processing of the material. Alongside this, recent methodological advancements, particularly in mass spectrometry are opening new opportunities for probing one of the most complex environmental mixtures. However, in order to fully exploit these opportunities, it is key that the way that samples are collected, processed and stored is considered carefully such that sample integrity is maintained. There are additional challenges when collecting water samples for analysis at molecular scale, for example the ultra-low concentrations of individual compounds within DOM means that the samples are sensitive to contamination. This paper discusses current sample collection, processing and storage protocols for this C, N and P quantification and characterisation in freshwaters, and proposes a new standardised protocol suitable for both nutrient fraction quantification and molecular scale analyses, based on method development and testing undertaken in our UK Natural Environment Research Council large grant programme, characterising the nature, origins and ecological significance of Dissolved Organic Matter IN freshwater Ecosystems (DOMAINE).

Microbial communities in crude oil phase and filter-graded aqueous phase from a Daqing oilfield after polymer flooding

AIMS

The aim was to characterize indigenous microorganisms in oil reservoirs after polymer flooding (RAPF).

METHODS

The microbial communities in the crude oil phase (Oil) and in the filter-graded aqueous phases Aqu0.22 (>0.22 μm) and Aqu0.1 (0.1~0.22 μm) were investigated by 16S rRNA gene high-throughput sequencing.

RESULTS

Indigenous microorganisms related to hydrocarbon degradation prevailed in the three phases of each well. However, obvious differences of bacterial compositions were observed among the three phases of the same well and among the same phase of different wells. The crude oil and Aqu0.22 shared many dominant bacteria. Aqu0.1 contained a unique bacterial community in each well. Most bacteria in Aqu0.1 were affiliated to culturable genera, suggesting that they may adapt to the oil reservoir environment by reduction of cell size. Contrary to the bacterial genera, archaeal genera were similar in the three phases but varied in relative abundances. The observed microbial differences may be driven by specific environmental factors in each oil well.

CONCLUSIONS

The results suggest an application potential of microbial enhanced oil recovery (MEOR) technology in RAPF. The crude oil and Aqu0.1 contain many different functional microorganisms related to hydrocarbon degradation. Both should not be overlooked when investing and exploring the indigenous microorganisms for MEOR.

SIGNIFICANCE AND IMPACT OF THE STUDY

This work facilitates the understanding of microbial community structures in RAPF and provides information for microbial control in oil fields.

Molecular characterization of dissolved organic nitrogen during anoxic/oxic and anammox processes using ESI FT-ICR MS

Dissolved organic nitrogen (DON) is a component of wastewater with a negative influence on the environment. The removal of DON is conducted through the anoxic/oxic (A/O) and anammox processes. However, the mechanisms and chemical preferences in the removal of DON compounds have not been understood and compared so far. This study, for the first time, comparatively investigated the molecular-level characteristics of DON during both processes by using FT-ICR MS (Fourier transform ion cyclotron resonance mass spectrometry). The results indicated that the number of DON formulas increased from 1844 to 1935 during A/O process, and from 2784 to 3242 during anammox process, highlighting the increase in complexity of DON after undergoing both processes. DON with high saturation and aliphatic structures was removed by A/O process, whereas highly unsaturated and aromatic structures were removed by anammox process. For DON without S atom, Lignin-like and tannin-like ones were resistant to both processes and protein-like and condensed aromatic structures were resistant to anammox process. The complementarity of these two processes provided a sequential combination with sufficient theoretical support to improve DON removal efficiency. PRACTITIONER POINTS: Molecular components of dissolved organic nitrogen characterized by ESI FT-ICR MS. DON removal preferences of A/O and anammox processes evaluated. A/O and anammox processes are effective to remove aliphatic and aromatic DON, respectively. Complementarity in removal preferences of A/O and anammox processes can remove recalcitrant DON of each other. Sequential A/O and anammox processes can improve DON removal.

Effect of different types of anthropogenic pollution on the bacterial community of urban rivers

The health of urban rivers is threatened by multiple anthropogenic stressors. Bacterial communities in rivers can quickly respond to different types of polluted environments, making them useful for water quality assessments and predictive insights. However, research on river bacterial communities has largely ignored interactions between these communities. Here, 16S rRNA amplicon sequencing analysis is used to comprehensively analyze the bacterial communities in the water and sediments in different types of anthropogenically impacted urban river. The results show that distinct differences occur in the bacterial communities in the river sediment and water with different pollution types. The changes in the bacterial communities in sediments were more pronounced than those in the water. A modular analysis further showed that the microbial co-occurrence network under different types of pollution had a nonrandom modular structure, and this structure was mainly driven by classification correlation and bacterial function. Genes identified for nitrogen cycling in all the river water and sediment samples included major functional genes for nitrogen fixation, assimilatory nitrogen reduction, nitrification, denitrification, and ammonification. Carbon degradation genes were mainly observed in the carbon cycle. Taken together, the above findings provide further insights into microbial communities in urban river ecosystems under anthropogenic contamination. PRACTITIONER POINTS: The physical and chemical indicators of the four types of pollution drive bacterial community structure. Bacterial community has C, N, P metabolic genes indicating its ecological effect. River bacteria were connected more frequently in the same or similar type of pollution in the co-occurrence network. Microbe-environment correlations and microbe-microbe interactions were combined to determine crucial indicators.

Optimising storage conditions and processing of sheep urine for nitrogen cycle and gaseous emission measurements from urine patches

In grazing systems, urine patches deposited by livestock are hotspots of nutrient cycling and the most important source of nitrous oxide (N2O) emissions. Studies of the effects of urine deposition, including, for example, the determination of country-specific N2O emission factors, require natural urine for use in experiments and face challenges obtaining urine of the same composition, but of differing concentrations. Yet, few studies have explored the importance of storage conditions and processing of ruminant urine for use in subsequent gaseous emission experiments. We conducted three experiments with sheep urine to determine optimal storage conditions and whether partial freeze-drying could be used to concentrate the urine, while maintaining the constituent profile and the subsequent urine-derived gaseous emission response once applied to soil. We concluded that filtering of urine prior to storage, and storage at - 20 °C best maintains the nitrogen-containing constituent profile of sheep urine samples. In addition, based on the 14 urine chemical components determined in this study, partial lyophilisation of sheep urine to a concentrate represents a suitable approach to maintain the constituent profile at a higher overall concentration and does not alter sheep urine-derived soil gaseous emissions.

Utilization of low-molecular-weight organic compounds by the filterable fraction of a lotic microbiome

Filterable microorganisms participate in dissolved organic carbon (DOC) cycling in freshwater systems, however their exact functional role remains unknown. We determined the taxonomic identity and community dynamics of prokaryotic microbiomes in the 0.22 µm-filtered fraction and unfiltered freshwater from the Conwy River (North Wales, UK) in microcosms and, using targeted metabolomics and 14C-labelling, examined their role in the utilization of amino acids, organic acids and sugars spiked at environmentally-relevant (nanomolar) concentrations. To identify changes in community structure, we used 16S rRNA amplicon and shotgun sequencing. Unlike the unfiltered water samples where the consumption of DOC was rapid, the filtered fraction showed a 3-day lag phase before the consumption started. Analysis of functional categories of clusters of orthologous groups of proteins (COGs) showed that COGs associated with energy production increased in number in both fractions with substrate addition. The filtered fraction utilized low-molecular-weight (LMW) DOC at much slower rates than the whole community. Addition of nanomolar concentrations of LMW DOC did not measurably influence the composition of the microbial community nor the rate of consumption across all substrate types in either fraction. We conclude that due to their low activity, filterable microorganisms play a minor role in LMW DOC processing within a short residence time of lotic freshwater systems.

Simultaneous changes of exogenous dissolved organic matter treated by ozonation in properties and interaction behavior with sulfonamides

Effluent is often treated with ozone before being discharged into a natural water environment. This process will change the interaction between effluent organic matter and pollutants in aquatic environment. The impact of ozonation on complexation between dissolved organic matter in such wastewater and sulfadimidine often found in natural water was studied in laboratory experiments using four types of real wastewater. Ozonation was found to decrease the proportion of organic matter with a molecular weight greater than 5 kDa as well as protein-like, fulvic-like and humic-like components, but except the proportion of hydrophilic components. The aromaticity of the dissolved organic matter was also reduced after ozonation. The complexation of tryptophan and tyrosine with sulfadimidine mainly depends on their hydrophobicity and large molecular weight. Ozonation of fulvic and humic acid tends to produce small and medium molecular weight hydrophilics. The complexation of humic and fulvic acids with sulfadimidine was enhanced by ozonation. Dissolved organic matter, with or without oxidation, were found to weaken sulfadimidine's inhibition of microbial growth, especially for Aeromonas and Acinetobacter species. This finding will expand our understanding about the impact of advanced treatment processes on the dissolved organic matters' properties in effluent.

Diverse molecular compositions of dissolved organic matter derived from different composts using ESI FT-ICR MS

Dissolved organic matter (DOM) derived from various composts can promote significant changes of soil properties. However, little is known about the DOM compositions and their similarities and differences at the molecular level. In this study, the molecular compositions of DOM derived from kitchen waste compost (KWC), green waste compost (GWC), manure waste compost (MWC), and sewage sludge compost (SSC) were characterized by electrospray ionization coupled with Fourier transform ion cyclotron resonance mass spectrometry (ESI FT-ICR MS). The molecular formulas were classified into four subcategories: CHO, CHON, CHOS, and CHONS. The KWC, MWC, and SSC DOM represented the highest fraction (35.8%-47.4%) of CHON subcategory, while the GWC DOM represented the highest fraction (68.4%) of CHO subcategory. The GWC DOM was recognized as the nitrogen- and sulfur-deficient compounds that were less saturated, more aromatic, and more oxidized compared with other samples. Further analysis of the oxygen, nitrogen-containing (N-containing), and sulfur-containing (S-containing) functional groups in the four subcategories revealed higher organic molecular complexity. Comparison of the similarities and differences of the four samples revealed 22.8% ubiquitous formulas and 17.4%, 11.1%, 10.7%, and 6.3% unique formulas of GWC, KWC, SSC, and MWC DOM, respectively, suggesting a large proportion of ubiquitous DOM as well as unique, source-specific molecular signatures. The findings presented herein provide new insight into the molecular characterization of DOM derived from various composts and demonstrated the potential role of these different compounds for agricultural utilization.

Plant source and soil interact to determine characteristics of dissolved organic matter leached into waterways from riparian leaf litter

Wetting of leaf litter accumulated in riparian zones during rainfall events provides pulses of dissolved organic matter (DOM) to rivers. Restoring riparian vegetation aims to reduce sediment and nutrient transport into rivers, however DOM from leaf litter can stimulate phytoplankton growth and interfere with water treatment processes. Improved understanding of the loads and chemical composition of DOM leached from leaf litter of different plant species, and how subsequent leaching through soils affects DOM retention or transformation, is needed to predict the outcomes of riparian revegetation. To investigate this, we simulated rapid leaching of rainfall through the leaf litter of two riparian tree species with and without subsequent leaching through soil, comparing dissolved organic carbon (DOC) and nitrogen (DON) loads, and DOM chemical composition (via spectroscopic and novel NMR-fingerprinting techniques). Plant source affected the load and composition of DOM leaching, with Eucalyptus tereticornis leaching more DOC than Casuarina cunninghamiana. Additionally, E. tereticornis DOM had a higher sugar, myo-inositol, benzoic acid, flavonoid and oxygenated aromatic content. More than 90% of leaf litter DOM was retained in the soil under simulated repeated heavy rainfall. The DOM chemistry of these species determined the total loads and changes in DOM composition leaching through soil. Less E. tereticornis DOM was retained by the soil than C. cunninghamiana DOM, with sugars, myo-inositol and amino acids being poorly retained compared to fatty acids and aromatic compounds. It also appears that DOM from E. tereticornis litter primed the soil, resulting in more DON being leached compared with bare soil. In comparison, C.cunninghamiana litter resulted in greater retention of DON, oxygenated aromatic compounds and the amino acid tryptophan. This study provides new information on how a range of DOM sources and transformations affect the DOM ultimately leached into waterways, key to developing improved models of DOM transformations in catchments.

Microbial uptake kinetics of dissolved organic carbon (DOC) compound groups from river water and sediments

Dissolved organic matter (DOM) represents a key component of carbon (C) cycling in freshwater ecosystems. While the behaviour of bulk dissolved organic carbon (DOC) in aquatic ecosystems is well studied, comparatively little is known about the turnover of specific DOC compounds. The aim of this study was to investigate the persistence of ¹⁴C-labelled low molecular weight (LMW) DOC at a wide range of concentrations (0.1 µM to 10 mM), in sediments and waters from oligotrophic and mesotrophic rivers within the same catchment. Overall, rates of DOC loss varied between compound groups (amino acids > sugars = organic acids > phenolics). Sediment-based microbial communities contributed to higher DOC loss from river waters, which was attributed, in part, to its greater microbial biomass. At higher DOC compound concentrations, DOC loss was greater in mesotrophic rivers in comparison to oligotrophic headwaters. A lag-phase in substrate use within sediments provided evidence of microbial growth and adaptation, ascribed here to the lack of inorganic nutrient limitation on microbial C processing in mesotrophic communities. We conclude that the higher microbial biomass and available inorganic nutrients in sediments enables the rapid processing of LMW DOC, particularly during high C enrichment events and in N and P-rich mesotrophic environments.

Nano-Sized and Filterable Bacteria and Archaea: Biodiversity and Function

Nano-sized and filterable microorganisms are thought to represent the smallest living organisms on earth and are characterized by their small size (50-400 nm) and their ability to physically pass through <0.45 μm pore size filters. They appear to be ubiquitous in the biosphere and are present at high abundance across a diverse range of habitats including oceans, rivers, soils, and subterranean bedrock. Small-sized organisms are detected by culture-independent and culture-dependent approaches, with most remaining uncultured and uncharacterized at both metabolic and taxonomic levels. Consequently, their significance in ecological roles remain largely unknown. Successful isolation, however, has been achieved for some species (e.g., Nanoarchaeum equitans and "Candidatus Pelagibacter ubique"). In many instances, small-sized organisms exhibit a significant genome reduction and loss of essential metabolic pathways required for a free-living lifestyle, making their survival reliant on other microbial community members. In these cases, the nano-sized prokaryotes can only be co-cultured with their 'hosts.' This paper analyses the recent data on small-sized microorganisms in the context of their taxonomic diversity and potential functions in the environment.

Ultrafiltration for the Determination of Cu Complexed with Dissolved Organic Matters of Different Molecular Weight from a Eutrophic River, China

The molecular weight of dissolved organic matter (DOM) is one of the essential factors controlling the properties of metal complexes. A continuous ultrafiltration experiment was designed to study the properties of Cu complexes with different molecular weights in a river before and after eutrophication. The results showed that the concentration of DOM increased from 26.47 to 38.20 mg/L during the eutrophication process, however, DOM was still dominated by the small molecular weight fraction before and after eutrophication. The amount of Cu-DOM complexes increased with the increasing of molecular weight, however, the amounts of DOM-Cu complexes before eutrophication were higher than those after eutrophication. This is because DOM contained more -COOH and -OH before eutrophication and these functional groups are the active sites complexed with Cu.