Bacterial and archaeal phylogenetic diversity associated with swine sludge from an anaerobic treatment lagoon

The dynamic history of prokaryotic phyla: discovery, diversity and division

Here, I review the dynamic history of prokaryotic phyla. Following leads set by Darwin, Haeckel and Woese, the concept of phylum has evolved from a group sharing common phenotypes to a set of organisms sharing a common ancestry, with modern taxonomy based on phylogenetic classifications drawn from macromolecular sequences. Phyla came as surprising latecomers to the formalities of prokaryotic nomenclature in 2021. Since then names have been validly published for 46 prokaryotic phyla, replacing some established names with neologisms, prompting criticism and debate within the scientific community. Molecular barcoding enabled phylogenetic analysis of microbial ecosystems without cultivation, leading to the identification of candidate divisions (or phyla) from diverse environments. The introduction of metagenome-assembled genomes marked a significant advance in identifying and classifying uncultured microbial phyla. The lumper-splitter dichotomy has led to disagreements, with experts cautioning against the pressure to create a profusion of new phyla and prominent databases adopting a conservative stance. The Candidatus designation has been widely used to provide provisional status to uncultured prokaryotic taxa, with phyla named under this convention now clearly surpassing those with validly published names. The Genome Taxonomy Database (GTDB) has offered a stable, standardized prokaryotic taxonomy with normalized taxonomic ranks, which has led to both lumping and splitting of pre-existing phyla. The GTDB framework introduced unwieldy alphanumeric placeholder labels, prompting recent publication of over 100 user-friendly Latinate names for unnamed prokaryotic phyla. Most candidate phyla remain 'known unknowns', with limited knowledge of their genomic diversity, ecological roles, or environments. Whether phyla still reflect significant evolutionary and ecological partitions across prokaryotic life remains an area of active debate. However, phyla remain of practical importance for microbiome analyses, particularly in clinical research. Despite potential diminishing returns in discovery of biodiversity, prokaryotic phyla offer extensive research opportunities for microbiologists for the foreseeable future.

Comparison of anaerobic digestion of starch- and petro-based bioplastic under hydrogen-rich conditions

To identify an economically viable waste management system for bioplastics, thermoplastic starch (TPS) and poly(butylene adipate-co-terephthalate) (PBAT) were anaerobically digested under hydrogen (H2)/carbon dioxide (CO2) and nitrogen (N2) gas-purged conditions to compare methane (CH4) production and biodegradation. Regardless of the type of bioplastics, CH4 production was consistently higher with H2/CO2 than with N2. The highest amount of CH4 was produced at 307.74 mL CH4/g volatile solids when TPS digested with H2/CO2. A stepwise increased in CH4 yield was observed, with a nominal initial increment followed by accelerated methanogenesis conversion as H2 was depleted. This may be attributed to a substantial shift in the microbial structure from hydrogenotrophic methanogen (Methanobacteriales and Methanomicrobiales) to heterotrophs (Spirochaetia). In contrast, no significant change was observed with PBAT, regardless of the type of purged gas. TPS was broken down into numerous derivatives, including volatile fatty acids. TPS produced more byproducts with H2/CO2 (i.e., 430) than with N2 (i.e., 320). In contrast, differential scanning calorimetry analysis on PBAT revealed an increase in crystallinity from 10.20 % to 12.31 % and 11.36 % in the H2/CO2- and N2-purged conditions, respectively, after 65 days of testing. PBAT surface modifications were characterized via Fourier transform infrared spectroscopy and scanning electron microscopy. The results suggest that the addition of H2/CO2 can enhance the CH4 yield and increase the breakdown rate of TPS more than that of PBAT. This study provides novel insights into the CH4 production potential of two bioplastics with different biodegradabilities in H2/CO2-mediated anaerobic digestion systems.

Low biological phosphorus removal from effluents treated by slow sand filters

The legislation for environment protection requires strict controls of the wastewater releasing in water bodies. The wastewater treatment plants (WWTP) have been used for organic matter degradation; however, the residual total phosphorus (TP) removal has not been efficient. TP and nitrogen present in wastewater are associated to eutrophication of water bodies and algae growth. Therefore, this study discusses the efficiency of phosphorus removal by a slow filter (SF), complementary to a WWTP and the microbial community involved. The results showed that the use of SF, with or without macrophytes, is not suitable to remove TP. Spatial variation in microbial communities distributed in three distinct zones was identified in the SF. Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes covered the hydrolytic and fermentative bacteria. The acetogenesis, nitrification, and denitrification, as well as the removal of phosphorus from the effluent, were performed by representatives affiliated to different groups. Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria among these, Dokdonella sp., Frateuria sp., Comamonas sp., Diaphorobacter sp., Nitrosospira sp., Ferruginibacter sp., Flavobacterium sp., and the uncultured OD1 were the most abundant bacteria in the SF. The low efficiency for TP removing from SF effluents can be explained by the low abundance of phosphorus accumulating organisms (PAOs), with the association of the low concentration of biodegradable organic matter in the inlet effluent. Therefore, the alternative to using SF as a complement to WWTPs, as recommended by some Brazilian environmental agencies, did not prove to be viable and new approaches must be evaluated. KEY POINTS: • The phosphorus removal was performed by a slow filter system in a WWTP but obtained a low efficiency. • Microbial spatial variation was distributed into distinct zones from slow filter. • Low abundance of PAOs was observed due to the low availability of organic matter.

Phylogeny, distribution and potential metabolism of candidate bacterial phylum KSB1

Candidate phylum KSB1 is composed of uncultured bacteria and has been reported across various environments. However, the phylogeny and metabolic potential of KSB1 have not been studied comprehensively. In this study, phylogenomic analysis of KSB1 genomes from public databases and eleven metagenome-assembled genomes (MAGs) from marine and hydrothermal sediments revealed that those genomes were clustered into four clades. Isolation source and relative abundance of KSB1 genomes showed that clade I was particularly abundant in bioreactor sludge. Genes related to dissimilatory reduction of nitrate to ammonia (DNRA), the last step of denitrification converting nitrous oxide to nitrogen and assimilatory sulfur reduction were observed in the expanded genomes of clade I, which may due to horizontal gene transfer that frequently occurred in bioreactor. Annotation and metabolic reconstruction of clades II and IV showed flagellum assembly and chemotaxis genes in the genomes, which may indicate that exploration and sensing for nutrients and chemical gradients are critical for the two clades in deep-sea and hydrothermal sediment. Metabolic potentials of fatty acids and short-chain hydrocarbons utilization were predicted in clades I and IV of KSB1. Collectively, phylogenomic and metabolic analyses of KSB1 clades provide insight into their anaerobic heterotrophic lifestyle and differentiation in potential ecological roles.

Destruction of the soil microbial ecological environment caused by the over-utilization of the rice-crayfish co-cropping pattern

The rice-crayfish co-cropping pattern is a traditional method for the intensive utilization of rice fields. In recent years, this pattern has been over-developed in many countries and regions, especially in China, because of its simple agronomic technology and high economic benefits. However, little is known about the potential ecological problems regarding soil microorganisms caused by the over-utilization of this pattern. The results show that rice-crayfish co-cropping, when over-utilized for a long time, reduced soil microbial richness and diversity compared with rice monocropping. A decrease in bacterial abundance in the nitrogen cycle and an increase in bacterial abundance in the carbon cycle led to a decrease in the nitrogen cycle function and an increase in the carbon cycle function. In an analysis of bacteria that are sensitive to cropping patterns, it was found that in the rice-crayfish co-cropping, the relative abundances of sensitive OTUs from Firmicutes (Bacillus and Clostridium) and Chloroflexi (Anaerolineaceae) were significantly higher during the entire growth period than those observed in the rice monocropping pattern, while the relative abundances of sensitive OTUs from Nitrospirae (Nitrospira), Gemmatimonadetes (Gemmatimonas), and Actinobacteria (Nocardioides) were significantly lower than those observed in the rice monocropping pattern. A network analysis shows that growth-period-sensitive OTUs drive the co-occurrence network modules, although the OTUs also have positive and negative correlations among modules but a positive synergistic effect on the regulation of soil nutrients. In addition, OTUs that were sensitive at the booting stage and filling stage were the key microbial groups in the rice-crayfish co-cropping and rice monocropping networks, respectively. Understanding the classifications and functions of sensitive microbes present during the rice growth period is the basis for formulating a microbial flora management strategy for the rice-crayfish co-cropping pattern, which is of great significance for adjusting agricultural management measures and controlling current soil microbial ecological problems.

Biological wastewater treatment (anaerobic-aerobic) technologies for safe discharge of treated slaughterhouse and meat processing wastewater

Slaughterhouse industry generates considerable amount of wastewater rich in proteins, lipids, fibres, and carbohydrates. Numerous technologies such as electrocoagulation, membrane separation, advanced oxidation, physico-chemical processes, and biological treatment have been implemented for reducing the concentrations of these compounds. Nevertheless, this review aims to provide extensive information solely on the biological treatment (anaerobic and aerobic) of slaughterhouse wastewater. The advantages of anaerobic treatment are excellent organic matter removal, less sludge production, low energy requirement, execution of higher loading rates, and considerable production of biogas. Aerobic treatment on the other hand is a less sensitive process, possess lower start-up period, and efficient nutrient removal process. Numerous case studies are described to bestow maximum understanding of the wastewater characteristics, kind of treatment employed, and complications involved in managing and treating of slaughterhouse effluent. Additionally, role of microbial community involved in the treatment of slaughterhouse waste is also discussed. Sequential anaerobic and aerobic reactors are also reviewed in order to present their advantages over single bioreactors. Intermittent sequencing batch reactor is a promising technology than other high rate digesters in the removal of carbon, nitrogen, and phosphorous.

Effects of a pulsed electric field on nitrogen removal through the ANAMMOX process at room temperature

This study explored the effect of a pulsed electric field (PEF) on the anaerobic ammonium oxidation (ANAMMOX) process at room temperature (20 ± 1 °C). The influences of different modes of PEF (R1), a direct current electric field (R2) and a control reactor (R3) were determined through long-term tests. The results showed that R1 shortened the start-up time and led to excellent nitrogen removal. At this stage, the activities of key enzymes of R1 were much higher than those of R3. The high-throughput sequencing results showed that the relative abundance of functional bacteria in R1 was higher than that in R2 and R3. The mechanism by which the PEF enhanced ANAMMOX might be the improvement of the speed of ion and molecular migration that occurred by changing the permeability of the cell membrane under the PEF.

Nitrogen removal of anaerobically digested swine wastewater by pilot-scale tidal flow constructed wetland based on in-situ biological regeneration of zeolite

Dispersed swine wastewater has increasingly aggravated water pollution in China. Anaerobically digested dispersed swine wastewater was targeted and treated by a pilot-scale zoning tidal flow constructed wetland (TFCW) with a bottom wastewater saturation layer. The long-term application of in-situ biological regeneration of biozeolite, nitrogen removal performance, nitrogen removal pathways and microbial community of TFCW were investigated. Results showed that with the surface loads of 0.079, 0.022 and 0.024 kg/(m²·d), TFCW could decrease COD, NH₄N and TN by 84.75%, 74.13% and 67.13% respectively. Influent COD, NH₄N, TN and nitrates/nitrites produced by bioregeneration of NH₄N were mostly removed in zeolite layer and the remaining nitrates/nitrites could be further denitrified in bottom saturation layer. Theory of dynamic process of rapid-adsorption and bioregeneration for NH₄N removal was proposed. When this process reached dynamic equilibrium, the mass of adsorbed NH₄N onto zeolites remained relatively stable. When ambient temperature decreased to 16 °C, TFCW could still remove COD, NH₄N and TN by 73.79%, 72.99% and 70.71% with the surface loads of 0.103, 0.056 and 0.054 kg/(m²·d) respectively. Nitrification-denitrification which accounted for 80.32% of TN removal was the main nitrogen removal pathway. Dominant nitrifiers (Nitrosospira and Rhizomicrobium) and denitrifiers (Ottowia, Thauera and Rhodanobacteria) in biozeolite layer verified the existence of simultaneous nitrification and denitrification.

Elevational characteristics of the archaeal community in full-scale activated sludge wastewater treatment plants at a 3,660-meter elevational scale

Due to the important roles of archaea in wastewater treatment processes, archaeal communities have been studied extensively in various anaerobic reactors, but the knowledge of archaeal communities in full-scale activated sludge wastewater treatment plants (WWTPs) remains quite poor. In this study, 454-pyrosequencing was for the first time employed to investigate archaeal communities from 20 full-scale activated sludge WWTPs distributed at a 3,660-meter elevational scale in China. Results showed that archaeal communities from WWTPs were dominated by Methanosarcinales (84.6%). A core archaeal population (94.5%) composed of Methanosaeta, Methanosarcina, Methanogenium and Methanobrevibacter was shared among WWTPs. The elevational pattern of archaeal communities was observed in WWTPs, with an elevational threshold associated with archaeal community richness and structures at approximately 1,500 meters above sea level (masl). A declining trend in community richness with increasing elevation was observed at higher elevations, whereas no trend was presented at lower elevations. Spearman correlation analysis indicated that the archaeal community richness at higher elevations was associated with more environmental variables than that at lower elevations. Redundancy analysis indicated that wastewater variables were the dominant contributors to the variation of community structures at higher elevations, followed by operational variables and elevation.

Effects of dissolved oxygen on performance and microbial community structure in a micro-aerobic hydrolysis sludge in situ reduction process

A sludge process reduction activated sludge (SPRAS), with a sludge process reduction module composed of a micro-aerobic tank and a settler positioned before conventional activated sludge process, showed good performance of pollutant removal and sludge reduction. Two SPRAS systems were operated to investigate effects of micro-aeration on sludge reduction performance and microbial community structure. When dissolved oxygen (DO) concentration in the micro-aerobic tank decreased from 2.5 (SPH) to 0.5 (SPL) mg/L, the sludge reduction efficiency increased from 42.9% to 68.3%. Compared to SPH, activated sludge in SPL showed higher contents of extracellular polymeric substances and dissolved organic matter. Destabilization of floc structure in the settler, and cell lysis in the sludge process reduction module were two major reasons for sludge reduction. Illumina-MiSeq sequencing showed that microbial diversity decreased under high DO concentration. Proteobacteria, Bacteroidetes and Chloroflexi were the most abundant phyla in the SPRAS. Specific comparisons down to the class and genus level showed that fermentative, predatory and slow-growing bacteria in SPL community were more abundant than in SPH. The results revealed that micro-aeration in the SPRAS improved hydrolysis efficiency and enriched fermentative and predatory bacteria responsible for sludge reduction.

Comparison of bacterial diversity in full scale anammox bioreactors operated under different conditions

Bacterial community structure of full-scale anammox bioreactor is still mainly unknown. It has never been analyzed whether different anammox bioreactor configurations might result in the development of different bacterial community structures among these systems. In this work, the bacterial community structure of six full-scale autotrophic nitrogen removal bioreactors located in The Netherlands and China operating under three different technologies and with different influent wastewater characteristics was studied by the means of pyrotag sequencing evaluation of the bacterial assemblage yielded a great diversity in all systems. The most represented phyla were the Bacteroidetes and the Proteobacteria, followed by the Planctomycetes. 14 OTUs were shared by all bioreactors, but none of them belonged to the Brocadiales order. Statistical analysis at OTU level showed that differences in the microbial communities were high, and that the main driver of the bacterial assemblage composition was different for the distinct phyla identified in the six bioreactors, depending on bioreactor technology or influent wastewater characteristics.

Biogas production and methanogenic archaeal community in mesophilic and thermophilic anaerobic co-digestion processes

Over 258 Mt of solid waste are generated annually in Europe, a large fraction of which is biowaste. Sewage sludge is another major waste fraction. In this study, biowaste and sewage sludge were co-digested in an anaerobic digestion reactor (30% and 70% of total wet weight, respectively). The purpose was to investigate the biogas production and methanogenic archaeal community composition in the anaerobic digestion reactor under meso- (35-37 °C) and thermophilic (55-57 °C) processes and an increasing organic loading rate (OLR, 1-10 kg VS m(-3) d(-1)), and also to find a feasible compromise between waste treatment capacity and biogas production without causing process instability. In summary, more biogas was produced with all OLRs by the thermophilic process. Both processes showed a limited diversity of the methanogenic archaeal community which was dominated by Methanobacteriales and Methanosarcinales (e.g. Methanosarcina) in both meso- and thermophilic processes. Methanothermobacter was detected as an additional dominant genus in the thermophilic process. In addition to operating temperatures, the OLRs, the acetate concentration, and the presence of key substrates like propionate also affected the methanogenic archaeal community composition. A bacterial cell count 6.25 times higher than archaeal cell count was observed throughout the thermophilic process, while the cell count ratio varied between 0.2 and 8.5 in the mesophilic process. This suggests that the thermophilic process is more stable, but also that the relative abundance between bacteria and archaea can vary without seriously affecting biogas production.

Microbial community analysis of swine wastewater anaerobic lagoons by next-generation DNA sequencing

Anaerobic lagoons are a standard practice for the treatment of swine wastewater. This practice relies heavily on microbiological processes to reduce concentrated organic material and nutrients. Despite this reliance on microbiological processes, research has only recently begun to identify and enumerate the myriad and complex interactions that occur in this microbial ecosystem. To further this line of study, we utilized a next-generation sequencing (NGS) technology to gain a deeper insight into the microbial communities along the water column of four anaerobic swine wastewater lagoons. Analysis of roughly one million 16S rDNA sequences revealed a predominance of operational taxonomic units (OTUs) classified as belonging to the phyla Firmicutes (54.1%) and Proteobacteria (15.8%). At the family level, 33 bacterial families were found in all 12 lagoon sites and accounted for between 30% and 50% of each lagoon's OTUs. Analysis by nonmetric multidimensional scaling (NMS) revealed that TKN, COD, ORP, TSS, and DO were the major environmental variables in affecting microbial community structure. Overall, 839 individual genera were classified, with 223 found in all four lagoons. An additional 321 genera were identified in sole lagoons. The top 25 genera accounted for approximately 20% of the OTUs identified in the study, and the low abundances of most of the genera suggests that most OTUs are present at low levels. Overall, these results demonstrate that anaerobic lagoons have distinct microbial communities which are strongly controlled by the environmental conditions present in each individual lagoon.