Changes in biofilm bacterial communities in response to combined effects of hypoxia, ocean acidification and nutrients from aquaculture activity in Three Fathoms Cove

Microbiome analysis reveals alteration in water microbial communities due to livestock activities

The Baihe River, a tributary of the Yellow River located in the Ngawa Tibetan and Qiang Autonomous Prefecture in Northern Sichuan, is surrounded by natural resources suitable for animal development. However, the impact of livestock activities water microbiome in this area remains unexplored. This study collected water samples from areas with captive yaks and sheep (NS and YS) and compared them with water samples from Hongyuan Baihe River. Through amplicon sequencing, we investigated the impact of livestock activities on aquatic microorganisms. Diversity analysis, significance analysis, and microbial phenotype prediction indicated a significant decrease in microbial community diversity and function in the NS and YS groups. Pathogenic microorganisms such as Bacteroidales and Thelebolaceae and antibiotic-resistant bacteria genes such as Flavobacteriales and Burkholderiaceae were significantly higher in livestock breeding areas. Additionally, bacteria adapted to acidification, hypoxia, and eutrophication (e.g., Acidobacteria, Flavobacteriales, Deltaproteobacteria, Rhodobacterales) were more abundant in these areas. Our results demonstrate that livestock activities significantly alter the structure and function of microbial communities in surrounding water bodies, deteriorating water quality.

Comprehensive review on recent trends and perspectives of natural exo-polysaccharides: Pioneering nano-biotechnological tools

Exopolysaccharides (EPSs), originating from various microbes, and mushrooms, excel in their conventional role in bioremediation to showcase diverse applications emphasizing nanobiotechnology including nano-drug carriers, nano-excipients, medication and/or cell encapsulation, gene delivery, tissue engineering, diagnostics, and associated treatments. Acknowledged for contributions to adsorption, nutrition, and biomedicine, EPSs are emerging as appealing alternatives to traditional polymers, for biodegradability and biocompatibility. This article shifts away from the conventional utility to delve deeply into the expansive landscape of EPS applications, particularly highlighting their integration into cutting-edge nanobiotechnological methods. Exploring EPS synthesis, extraction, composition, and properties, the discussion emphasizes their structural diversity with molecular weight and heteropolymer compositions. Their role as raw materials for value-added products takes center stage, with critical insights into recent applications in nanobiotechnology. The multifaceted potential, biological relevance, and commercial applicability of EPSs in contemporary research and industry align with the nanotechnological advancements coupled with biotechnological nano-cleansing agents are highlighted. EPS-based nanostructures for biological applications have a bright future ahead of them. Providing crucial information for present and future practices, this review sheds light on how eco-friendly EPSs derived from microbial biomass of terrestrial and aquatic environments can be used to better understand contemporary nanobiotechnology for the benefit of society.

Novel strategy for treating high salinity oilfield produced water: Pyrite-activated peroxymonosulfate coupled with heterotrophic ammonia assimilation

Existing conventional biological treatment techniques face numerous limitations in effectively removing total petroleum hydrocarbons (TPHs) and ammonia (NH4+-N) from oilfield-produced water (OPW), highlighting the pressing need for innovative pre-oxidation and biological treatment processes. In this study, a pyrite-activated peroxymonosulfate (PMS)-coupled heterotrophic ammonia assimilation (HAA) system was established to achieve satisfactory system performance for OPW treatment. Pyrite sustained-release Fe2+-activated PMS was used to produce SO4•- and •OH, and 71.0 % of TPHs were effectively removed from the oil wastewater. The average TPHs and NH4+-N removal efficiencies in the test group with pre-oxidation were 96.9 and 98.3 %, compared to 46.5 and 77.1 % in the control group, respectively. The maximum fluorescence intensities of tryptophan protein and aromatic protein in the test group declined by 83.7 %. Fourier transform ion cyclotron resonance mass spectrometry revealed that pre-oxidation degraded more long-chain hydrocarbons and aromatic family compound, whereas the HAA process produced more proteins and carbohydrates. Pyrite-PMS promoted the enrichment of ammonia-assimilating bacteria, alleviating the explosive increase in extracellular polymeric substances and reducing sludge settleability. The low cost, efficiency, green chemistry principles, and synergies of this approach make it a powerful solution for practical OPW treatment to reduce environmental impacts and promote sustainable wastewater treatment.

Promoting effect of raft-raised scallop culture on the formation of coastal hypoxia

The coastal waters around the Yangma Island are an important mariculture area of raft-raised scallop and bottom-seeded sea cucumber in the North Yellow Sea, China. Large-scale hypoxia in the bottom water of this area has caused the death of a large number of sea cucumbers and heavy economic losses. To find out the formation mechanism of hypoxia, the data obtained in each August during 2015-2018 were analyzed. Compared with the non-hypoxic year (2018), the temperature, trophic index (TRIX) and dissolved organic carbon (DOC) in the bottom water were relatively higher, and the water column was stratified causing by continuous high air temperature and low wind speed meteorological conditions in the hypoxic years (2015-2017). These sites with the coexistence of thermocline and halocline, and the thickness of thermocline >2.5 m and its upper boundary >7.0 m deep, were prone to hypoxia. Spatially, the hypoxic place was highly consistent with the scallop cultivating places, and the DOC, TRIX, NH₄⁺/NO₃^- and apparent oxygen utilization (AOU) at the culture sites were higher, indicating that organic matter and nutrients released by scallops may lead to local oxygen depletion. In addition, the bottom water of the culture sites had higher salinity, but lower turbidity and temperature, indicating that the slowed water exchange caused by scallop culture was a dynamic factor of hypoxia. All sites with AOU >4 mg/L at the bottom had hypoxia occurrence, even if there was no thermocline. In other words, stratification promoted the formation of hypoxia in coastal bottom water, but it was not indispensable. The raft-raised scallop culture could promote the formation of coastal hypoxia, which should arouse the attention for other coastal areas with intensive bivalve production.

Compact and automated eDNA sampler for in situ monitoring of marine environments

Using environmental DNA (eDNA) to monitor biodiversity in aquatic environments is becoming an efficient and cost-effective alternative to other methods such as visual and acoustic identification. Until recently, eDNA sampling was accomplished primarily through manual sampling methods; however, with technological advances, automated samplers are being developed to make sampling easier and more accessible. This paper describes a new eDNA sampler capable of self-cleaning and multi-sample capture and preservation, all within a single unit capable of being deployed by a single person. The first in-field test of this sampler took place in the Bedford Basin, Nova Scotia, Canada alongside parallel samples taken using the typical Niskin bottle collection and post-collection filtration method. Both methods were able to capture the same aquatic microbial community and counts of representative DNA sequences were well correlated between methods with R[Formula: see text] values ranging from 0.71-0.93. The two collection methods returned the same top 10 families in near identical relative abundance, demonstrating that the sampler was able to capture the same community composition of common microbes as the Niskin. The presented eDNA sampler provides a robust alternative to manual sampling methods, is amenable to autonomous vehicle payload constraints, and will facilitate persistent monitoring of remote and inaccessible sites.

Epibenthic microbial mats behavior as phosphorus sinks or sources in relation to biological and physicochemical conditions

Microbial mats are complex microecosystems that have shown promise as possible green filters to remediate polluted seawater. This usage would possibly require changing the natural conditions under which these microbial mats prosper in order to maximize their contact with the water. Thus, it is necessary to evaluate the adaptation of the mats to different environmental conditions, while monitoring their short-term efficiency at nutrient removal. To that aim, epibenthic microbial mats collected from a tidal flat in the Bahía Blanca Estuary, were incubated under different flooding conditions (periodically exposed to the air or continuously flooded), with and without the addition of a high phosphorus concentration (5 mg PO₄^3- L^-1), and with and without the presence of penicillin. This last condition was added to understand the influence of penicillin-sensitive microbes on cyanobacteria and diatom communities and their importance for P remediation. The presence of high P concentrations as well as the continual flooding of the mats resulted in the decrease of the dominant cyanobacterium, Coleofasciculus (Microcoleus) chthonoplastes, giving rise to the dominance of other genera such as Arthrospira sp. Or Oscillatoria sp., depending on the presence or absence of the antibiotic, respectively. Water P removal was highly efficient (60-87%) when the mats were treated with the high-P water. However, microbial mat behavior changed from P sink to source when mats where incubated in seawater with no P addition, suggesting that mats can both function as P sinks and sources, depending on the condition of the water they come in contact with.

Genome-centric metagenomics reveals insights into the evolution and metabolism of a new free-living group in Rhizobiales

Background

The Rhizobiales (Proteobacteria) order is an abundant and diverse group of microorganisms, being extensively studied for its lifestyle based on the association with plants, animals, and humans. New studies have demonstrated that the last common ancestor (LCA) of Rhizobiales had a free-living lifestyle, but the phylogenetic and metabolism characterization of basal lineages remains unclear. Here, we used a high-resolution phylogenomic approach to test the monophyly of the Aestuariivirgaceae family, a new taxonomic group of Rhizobiales. Furthermore, a deep metabolic investigation provided an overview of the main functional traits that can be associated with its lifestyle. We hypothesized that the presence of pathways (e.g., Glycolysis/Gluconeogenesis) and the absence of pathogenic genes would be associated with a free-living lifestyle in Aestuariivirgaceae.

Results

Using high-resolution phylogenomics approaches, our results revealed a clear separation of Aestuariivirgaceae into a distinct clade of other Rhizobiales family, suggesting a basal split early group and corroborate the monophyly of this group. A deep functional annotation indicated a metabolic versatility, which includes putative genes related to sugar degradation and aerobic respiration. Furthermore, many of these traits could reflect a basal metabolism and adaptations of Rhizobiales, as such the presence of Glycolysis/Gluconeogenesis pathway and the absence of pathogenicity genes, suggesting a free-living lifestyle in the Aestuariivirgaceae members.

Conclusions

Aestuariivirgaceae (Rhizobiales) family is a monophyletic taxon of the Rhizobiales with a free-living lifestyle and a versatile metabolism that allows these microorganisms to survive in the most diverse microbiomes, demonstrating their adaptability to living in systems with different conditions, such as extremely cold environments to tropical rivers.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-021-02354-4.

Comparison of different cultures and culturing conditions for the biological deterioration of organic load from real saline bilge wastewater: microbial diversity insights and ecotoxicity assessment

Bilge wastewater is a high strength, typically saline wastewater, originating from operation of ships. In this study, the treatment of real bilge wastewater was tested using pure isolated aerobic strains and mixed cultures (aerobic and anaerobic). The Chemical Oxygen Demand (COD) and ecotoxicity decrease were monitored over time, while the microbial dynamics alterations in mixed cultures were also recorded. The isolated strains Pseudodonghicola xiamenensis, Halomonas alkaliphila and Vibrio antiquaries were shown to significantly biodegrade bilge wastewater. Reasonable COD removal rates were achieved by aerobic mixed cultures (59%, 9 days), while anaerobic mixed cultures showed lower performance (34%, 51 days). The genus Pseudodonghicola was identified as dominant under aerobic conditions both in the mixed cultures and in the control sample (raw wastewater), after exposure to bilge wastewater, demonstrating natural proliferation of the genus and potential contribution to COD reduction. Biodegradation rates were higher when initial organic load was high, while the toxicity of raw wastewater partially decreased after treatment.

Potential linkage between sedimentary oxygen consumption and benthic flux of biogenic elements in a coastal scallop farming area, North Yellow Sea

Surface sediments were collected from a mariculture area adjacent to the Yangma Island suffering from hypoxia in summer, and a laboratory static incubation was conducted to study the sedimentary oxygen consumption (SOC) and the benthic fluxes of nutrients and fluorescent dissolved organic matter (FDOM). Compared with some coastal areas, the SOC of the studied area was relatively low in summer with the value of 2.34-6.03 mmol m^-2 d^-1. Sediment acted as an important source of nutrients (except for nitrate) and FDOM for the overlying water. Dissolved oxygen (DO) in the overlying water could affect the decomposition mode of sedimentary organic matter (SOM), i.e. aerobic and anaerobic decomposition and subsequently dominated the release of nutrients and FDOM. When DO > 50 μmol l^-1, it was beneficial to the release of ammonium, silicate and FDOM. In contrast, low oxygen conditions, i.e. DO < 100 μmol l^-1, stimulated sediment phosphate efflux. In addition, scallop farming activities also affected the SOC and benthic flux of nutrients and FDOM mainly through biological deposition.

Photoprotection and antioxidative metabolism in Ulva lactuca exposed to coastal oceanic acidification scenarios in the presence of Irgarol

Anthropogenic changes such as ocean acidification, eutrophication, and the release of hazardous chemicals affect coastal environments and aquatic organisms. We investigated the effects of seawater pH (7.4 and 8.2) isolated and in combination with Irgarol on Ulva lactuca. Stress indicators such as membrane damage, lipid peroxidation, and hydrogen peroxide content were assessed. In addition, chlorophyll fluorescence and antioxidant enzyme activities were measured. The photosynthetic yield was affected by low pH in assays with and without Irgarol. However, the combination of low pH and Irgarol promoted photoinhibition, besides the induction of non-photochemical quenching (NPQ) and changes in photosynthetic pigment contents. The induction of NPQ was directly influenced by low pH. The membrane damage was increased in low pH with and without Irgarol exposure. Total soluble protein and carbohydrate contents decreased in low pH, and in presence of Irgarol. The H₂O₂ content and lipid peroxidation were not affected by low pH. In contrast, Irgarol exposure strongly increased lipid peroxidation in both pHs, suggesting a possible synergistic effect. To avoid the harmful effects of high H₂O₂, U. lactuca increased antioxidant enzyme activities in treatments under low pH and in presence of Irgarol. Our results indicate that U. lactuca is tolerant to low pH by inducing NPQ, changing pigment contents, and increasing antioxidant defenses. In contrast, these protective mechanisms could not avoid the harmful effects of the combination with Irgarol.

Use of ecological concrete for nutrient removal in coastal sediment and its effects on sediment microbial communities

Ecological concrete (eco-concrete) can reduce excess nutrients (nitrogen and phosphorus) in water, but its effectiveness in removing nutrients in marine coastal sediments and the response of sediment microbial communities to its use are largely unknown. In this study, eco-concrete planted with Bruguiera gymnorrhiza was used to remove nutrients in marine coastal sediment. We found that the mean removal efficiencies of sediment total nitrogen and total phosphorus by using planted eco-concrete were 11.50% and 30.31% on day 60, and were higher than those obtained by only using B. gymnorrhiza (7.14% and 7.36%). the Diatoms and bacterial genera Fusibacter and Anoxynatronum (which belong to Firmicutes) increased and became the abundant microbes by day 60 when using planted eco-concrete, indicating their potential roles in nutrient removal. Moreover, the eco-concrete did not endanger the core microbes in sediment suggesting its environment-friendly character. Our results suggest a potential method to control marine coastal eutrophication.