Effects of bacterial-feeding nematodes on soil microbial activity and the microbial community in oil-contaminated soil

Temporal assembly patterns of microbial communities in three parallel bioreactors treating low-concentration coking wastewater with differing carbon source concentrations

Carbon source is an important factor of biological treatment systems, the effects of which on their temporal community assembly patterns are not sufficiently understood currently. In this study, the temporal dynamics and driving mechanisms of the communities in three parallel bioreactors for low-concentration coking wastewater (CWW) treatment with differing carbon source concentrations (S0 with no glucose addition, S1 with 200 mg/L glucose addition and S2 with 400 mg/L glucose addition) were comprehensively studied. High-throughput sequencing and bioinformatics analyses including network analysis and Infer Community Assembly Mechanisms by Phylogenetic bin-based null model (iCAMP) were used. The communities of three systems showed turnover rates of 0.0029∼0.0034 every 15 days. Network analysis results showed that the S0 network showed higher positive correlation proportion (71.43%) and clustering coefficient (0.33), suggesting that carbon source shortage in S0 promoted interactions and cooperation of microbes. The neutral community model analysis showed that the immigration rate increased from 0.5247 in S0 to 0.6478 in S2. The iCAMP analysis results showed that drift (45.89%) and homogeneous selection (31.68%) dominated in driving the assembly of all the investigated microbial communities. The contribution of homogeneous selection increased with the increase of carbon source concentrations, from 27.92% in S0 to 36.08% in S2. The OTUs participating in aerobic respiration and tricarboxylic acid (TCA) cycle were abundant among the bins mainly affected by deterministic processes, while those related to the metabolism of refractory organic pollutants in CWW such as alkanes, benzenes and phenols were abundant in the bins dominated by stochastic processes.

Soil fauna-microbial interactions shifts fungal and bacterial communities under a contamination disturbance

The aim of this study was to determine whether the soil faunal-microbial interaction complexity (SFMIC) is a significant factor influencing the soil microbial communities and the willow growth in the context of PAH contamination. The SFMIC treatment had eight levels: just the microbial community, or the microbial community with nematodes, springtails, earthworms and all the possible combinations. SFMIC affected the height and biomass of willows after eight weeks or growth. SFMIC affected the structure and the composition of the bacterial, archaeal and fungal communities, with significant effects of SFMIC on the relative abundance of fungal genera such as Sphaerosporella, a known willow symbiont during phytoremediation, and bacterial phyla such as Actinobacteriota, containing many polycyclic aromatic hydrocarbons (PAH) degraders. These SFMIC effects on microbial communities were not clearly reflected in the community structure and abundance of PAH degraders, even though some degraders related to Actinobacteriota and the diversity of Gram-negative degraders were affected by the SFMIC treatments. Over 95% of PAH was degraded in all pots at the end of the experiment. Overall, our results suggest that, under our experimental conditions, SFMIC changes willow phytoremediation outcomes.

Responses of the root morphology and photosynthetic pigments of ryegrass to fertilizer application under combined petroleum-heavy metal stress

With developments in industry, petroleum and heavy metal pollution are increasingly affecting soil, significantly harming the environment, biosecurity, and human health. Therefore, the remediation of contaminated soil is becoming increasingly important. In this study, ryegrass (Lolium perenne L.) was planted in petroleum-heavy metal co-contaminated soil with the application of nitrogen and phosphorus fertilizers. Three treatments were set up: uncontaminated soil + ryegrass (SH); petroleum-heavy metal co-contaminated soil + ryegrass (SPGH); and petroleum-heavy metal co-contaminated soil + ryegrass + nitrogen and phosphorus fertilizer (SPGH + NP). The results showed that the petroleum-heavy metal co-contamination promoted increases in the root length, surface area, volume, and diameter of ryegrass roots, increasing the below-ground biomass and decreasing the photosynthetic pigment content in the early stages of the experiment. The ratios of chlorophyll a/b and chlorophyll/carotenoid also increased. However, the application of fertilizer reduced the length, surface area, volume, and diameter of ryegrass roots in the co-contaminated soil, and the below-ground biomass decreased while the above-ground biomass increased. Furthermore, the photosynthetic pigment content was significantly higher than that in the unfertilized treatment and the chlorophyll a/b ratio decreased while the chlorophyll/carotenoid ratio increased. Therefore, fertilizers could alleviate the toxic effects of petroleum-heavy metal combined pollution on ryegrass roots and promote the synthesis of chlorophyll and other pigments, thus reducing the inhibitory effect of petroleum-heavy metal combined pollution on ryegrass growth and facilitating the remediation of the polluted soil.

Variation of microbial activities and communities in petroleum-contaminated soils induced by the addition of organic materials and bacterivorous nematodes

Bacterivorous nematodes are abundant in petroleum-contaminated soils. However, the ecological functions of bacterivorous nematodes and their impacts together with the addition of organic materials on the activity and diversity of microorganisms in petroleum-contaminated soils remain unknown. To assess such effects, six treatments were established in this study, including uncontaminated nematodes-free soil (Control), petroleum-contaminated soil (PC), petroleum-contaminated soil + 5 nematodes per gram dry soil (PCN), and petroleum-contaminated soil + 5 nematodes per gram dry soil + 1% wheat straw (PCNW), or + 1% rapeseed cake (PCNR), or + 1% biochar (PCNB). Results showed that the enzyme activities in the six treatments generally increased firstly and then decreased during the incubation period. Compared with Control, the invertase activity in PCNW, PCNR, and PCNB increased by 80.6%, 313.5%, and 12.4%, respectively, whereas the urease activity in PC, PCN, PCNW, PCNR, and PCNW increased by 1.2%, 25.5%, 124.3%, 105.3%, and 25.5%, respectively. Petroleum pollution, inoculation of bacterivorous nematodes, and the addition of organic materials all significantly boosted the concentrations of phospholipid fatty acids (PLFAs) of soil bacteria, actinobacteria, and total microorganisms, and increased the concentrations of both G⁺ and G^- bacteria PLFAs and the ratio of G^-/G⁺. The concentration of fungi PLFAs and the ratio of fungi to bacteria were significantly higher in PCNW and PCNR than those in other treatments. Overall, adding bacterivorous nematodes and organic materials to the petroleum-contaminated soil significantly improved soil microbial activity and community structure, suggesting that bacterivorous nematodes could be used for the bioremediation in petroleum contaminated soils.

Response of Soil Nematode Community Structure and Function to Monocultures of Pumpkin and Melon

It is well known that crop monoculture can induce negative effects on soil ecosystems and crop productivity. However, little is known about how vegetable monoculture affects the soil nematode community structure and its relationship with vegetable yields. In this study, the composition, abundance, metabolic footprint, and ecological indices of soil nematodes are investigated in monocultures of pumpkin and melon. The relationships between nematode community structure and yields of pumpkin and melon were analyzed by linear regression. Both monoculture soils of pumpkin and melon suppressed the relative abundance of bacterivores but increased the relative abundance of plant parasites. Pumpkin monoculture soils decreased soil nematode diversity but increased the maturity index of plant parasites. Monoculture soils of pumpkin and melon decreased the metabolic footprint of lower- and higher-level trophic groups of the soil food web, respectively. Pumpkin and melon monoculture soils increased the food web indices channel index (CI) but decreased the enrichment index (EI) and the structure index (SI). The monoculture soils of pumpkin and melon led to a more fungal-dominated decomposition pathway and degraded soil food web conditions. The abundance of bacterivores and food web indices EI and SI were positively correlated with soil nutrients and pH, while the abundance of plant parasites and CI were negatively correlated with soil nutrients and pH. Paratylenchus was negatively correlated with pumpkin and melon yields and could be the potential plant parasites threatening pumpkin and melon productions. Redundancy analysis showed that monocultures of pumpkin and melon altered the soil nematode community via soil properties; total N, total P, alkeline-N, and pH were the main driving factors.

Oil degradation and variation of microbial communities in contaminated soils induced by different bacterivorous nematodes species

Oil pollution poses a great threat to environments and makes the remediation of oil-contaminated soils an urgent task. Microorganisms are the main biological factor for oil removal in the environment but microbial remediation is greatly affected by environmental factors. For our research, we inoculated three species of bacterivorous nematodes into oil-contaminated soil to explore how bacterivorous nematodes affect soil microbial activities and community structure in contaminated soil, as well as how efficiently different nematodes remove oil pollution from the soil. Six treatments were set in this experiment: sterilized oil-contaminated soil (SOC); nematode-free soil (S); oil-contaminated soil (OC); oil-contaminated soil + Caenorhabditis elegans (OCN1); oil-contaminated soil + Cephalobus persegnis (OCN2); oil-contaminated soil + Rhabditis marina (OCN3) for a 168-day incubation experiment. After the experiment was done, the oil contents in SOC, OC, OCN1, OCN2, and OCN3 were reduced by 6.5%, 32.3%, 38.2%, 42.8%, and 40.2%, respectively, compared with the beginning of the experiment. The amount of phospholipid fatty acids (PLFAs) of Gram-negative bacteria in OC, OCN1, OCN2, and OCN3 was increased by 50.9%, 43.4%, 37.7%, and 47.9%, respectively, compared with that of S. During the 168-day incubation period, the maximum growth of the number of nematodes in OCN1, OCN2, and OCN3 compared with the initial number of the nematodes were 2.25-, 1.52-, and 1.65-fold, respectively. The amount of oil residue in the contaminated soil negatively correlated with the populations of nematodes, total microorganisms, Gram-negative bacteria, actinomycetes, and eukaryotes. Thus, oil pollution increased the number of Gram-negative bacteria, decreased the ratio of Gram-positive bacteria/Gram-negative bacteria and Fungi/Bacteria significantly, and altered the community structure of soil microorganisms. Each species of bacterivorous nematodes has got its unique effect on the microbial activity and community structure in oil contaminated soils, but those tested can promote oil degradation and thus improve the environment of oil contaminated soils.

Iron Flocs and the Three Domains: Microbial Interactions in Freshwater Iron Mats

Freshwater iron mats are dynamic geochemical environments with broad ecological diversity, primarily formed by the iron-oxidizing bacteria. The community features functional groups involved in biogeochemical cycles for iron, sulfur, carbon, and nitrogen. Despite this complexity, iron mat communities provide an excellent model system for exploring microbial ecological interactions and ecological theories in situ Syntrophies and competition between the functional groups in iron mats, how they connect cycles, and the maintenance of these communities by taxons outside bacteria (the eukaryota, archaea, and viruses) have been largely unstudied. Here, we review what is currently known about freshwater iron mat communities, the taxa that reside there, and the interactions between these organisms, and we propose ways in which future studies may uncover exciting new discoveries. For example, the archaea in these mats may play a greater role than previously thought as they are diverse and widespread in iron mats based on 16S rRNA genes and include methanogenic taxa. Studies with a holistic view of the iron mat community members focusing on their diverse interactions will expand our understanding of community functions, such as those involved in pollution removal. To begin addressing questions regarding the fundamental interactions and to identify the conditions in which they occur, more laboratory culturing techniques and coculture studies, more network and keystone species analyses, and the expansion of studies to more freshwater iron mat systems are necessary. Increasingly accessible bioinformatic, geochemical, and culturing tools now open avenues to address the questions that we pose herein.

Low-dose biochar added to sediment improves water quality and promotes the growth of submerged macrophytes

Biochar is a good adsorbent for water pollutants. However, the effects of biochar on aquatic organisms are not well understood. In this study, different amounts of biochar (CK, 0 mg/g; T1, 10 mg/g; T2, 30 mg/g) were added to sediment to study changes in water quality and its impact on three submerged macrophytes (Hydrilla verticillata, Vallisneria natans, and Ceratophyllum demersum) and the sediment microbial community. The results indicated that biochar treatments significantly increased the water pH and conductivity. Compared with the initial values, the total phosphorus (P) contents in the water of the CK, T1, and T2 treatments decreased by 78.5%, 95.0%, and 58.3%, respectively, while the total nitrogen contents increased by 26.26%, -5.81%, and 19.70%, respectively. Compared with those in CK, the relative growth rates of H. verticillata, V. natans, and C. demersum in T1 increased by 28.4%, 163.1%, and 61.3%, respectively, while those in T2 showed no significant difference except that the growth rates of H. verticillata decreased by 17.7%. The P contents of the three submerged macrophytes increased with the increase of biochar addition, except that there was no significant difference between T2 and CK for H. verticillata. Biochar treatments reduced the biomass of total microbial, bacterial, and fungal phospholipid fatty acids in the sediment for H. verticillata and V. natans, and they increased fungal: bacterial ratios in the low-dose biochar treatments for V. natans and C. demersum. This study demonstrates that the addition of biochar to sediment significantly increased the pH and conductivity, and decreased total P contents in the water. Low-dose biochar treatments were more beneficial for water quality improvements and the growth of submerged macrophytes than high-dose biochar.

Assessment of the Lowland Bog Biomass for Ex Situ Remediation of Petroleum-Contaminated Soils

Bog petroleum-contaminated soils have been remediated ex situ in conditions close to natural ones. It was found that during the first 30 days in natural conditions, the decomposition of total petroleum hydrocarbons (TPH) was 30 ± 5%. On the 60th and 90th days, the process of TPH decomposition was 45 ± 5% and 60 ± 5%, respectively. The effect of various stimulant supplements was negligible. For the entire observed period, bog soil showed a very high self-cleaning potential with pollution concentration of 5 g of petroleum per 100 g of soil sample. Such diagnostic indicators of soil condition as urease and cellulase activities turned out to be most sensitive in the bog soil. The introduction of mineral fertilizers to stimulate the TPH decomposition increased the activity of urease in comparison with the background soil. On the other hand, the nonionic surfactant acted as an inhibitor of microorganisms involved in nitrogen metabolism, even in the presence of mineral fertilizers. The introduction of mineral fertilizers to petroleum-polluted bog soil stimulated the cellulases activity, while surfactants suppressed them in the early stages. The simultaneous introduction of surfactants and fertilizers kept the cellulase activity at the background level. It is concluded that in the case of petroleum pollution of infertile soils, the introduction of the upper layers of the phytomass of lowland bogs by providing looseness and long-term supply of nutrients from the dying parts of the moss will accelerate the self-cleaning processes.