Lettuce (Lactuca sativa) productivity influenced by microbial inocula under nitrogen-limited conditions in aquaponics

Integrated rice-yellow catfish farming resulting in variations in the agricultural environment, rice growth performance, and soil bacterial communities

Different rice production patterns exert varying comprehensive impacts on the agricultural environment. Integrated rice-fish farming, an advanced and rapidly developing agricultural production pattern, aims to improve resource utilization efficiency and enhance food productivity. To unravel the responses and internal interactions of the agricultural ecological environment to integrated rice-fish farming, we assessed and compared environmental factor, rice growth performance, and soil microbiome in both integrated rice-yellow catfish farming (IRYF) and rice monoculture (RM) systems. Our results revealed significant increases in the total nitrogen and ammonia concentrations in the paddy water and soil induced by the IRYF. Rice growth performance in the IRYF group surpassed that in the RM group. IRYF obviously impacted almost all dominant bacterial phyla, genera, and functional groups (top ten most abundant), enhancing the ability of bacteria to degrade and utilize organic matter. Additionally, IRYF led to noticeable reductions in the Shannon, Simpson, Chao 1, and Pielou_J indices. IRYF strengthened the interconnections between various taxonomic units in bacterial co-occurrence network, resulting in increased complexity, stability, and disturbance resistance in the soil bacterial community. IRYF notably facilitated the transition from a community assembly dominated by stochastic processes to one dominated by deterministic processes for the soil bacterial community. The deterministic process driving this transition was variable selection. All the environmental factors, except for soil nitrate, demonstrated relatively high contributions to alterations in soil bacterial communities, with environmental variables significantly positively correlated with the soil bacterial community in the IRYF group. Alterations in functionality, composition, and diversity of the soil bacterial community were clearly associated with most environmental variables and rice growth performance indices. Our research contributed to understanding the comprehensive impacts of integrated rice-fish farming on agricultural ecosystems and provide theoretical support for achieving the sustainable agricultural production and optimizing the rice production patterns.

Influences of the Integrated Rice-Crayfish Farming System with Different Stocking Densities on the Paddy Soil Microbiomes

Integrated rice-fish farming has emerged as a novel agricultural production pattern to address global food security challenges. Aiming to determine the optimal, scientifically sound, and sustainable stocking density of red claw crayfish (Cherax quadricarinatus) in an integrated rice-crayfish farming system, we employed Illumina high-throughput 16S rRNA gene sequencing to evaluate the impact of different stocking densities of red claw crayfish on the composition, diversity, function, and co-occurrence network patterns of soil bacterial communities. The high stocking density of red claw crayfish reduced the diversity and evenness of the soil bacterial community during the mid-culture stage. Proteobacteria, Actinobacteria, and Chloroflexi emerged as the most prevalent phyla throughout the experimental period. Low stocking densities initially boosted the relative abundance of Actinobacteria in the paddy soil, while high densities did so during the middle and final stages. There were 90 distinct functional groups identified across all the paddy soil samples, with chemoheterotrophy and aerobic chemoheterotrophy being the most abundant. Low stocking densities initially favored these functional groups, whereas high densities enhanced their relative abundances in the later stages of cultivation. Medium stocking density of red claw crayfish led to a more complex bacterial community during the mid- and final culture stages. The experimental period showed significant correlations with soil bacterial communities, with total nitrogen (TN) and total phosphorus (TP) concentrations emerging as primary factors contributing to the alterations in soil bacterial communities. In summary, our findings demonstrated that integrated rice-crayfish farming significantly impacted the soil microbiomes and environmental factors at varying stocking densities. Our study contributed to theoretical insights into the profound impact of integrated rice-crayfish farming with various stocking densities on bacterial communities in paddy soils.

Inoculum and pH effects on ammonium removal and microbial community dynamics in aquaponics systems

Understanding the ecology of microorganisms is essential for optimizing aquaponics systems. Effects of pH and inoculum on ammonium removal and dynamics of microbial community composition from all compartments of lab-scale aquaponics systems were examined. Initial ammonium accumulation in systems with comammox-enriched inocula were 47% and 69% that of systems enriched with ammonia-oxidizing bacteria (AOB), with higher rates of ammonium removal and transient nitrite accumulation measured in the latter systems. By the end of operation, Nitrosomonas and Nitrosospira AOB were dominant nitrifiers in systems at pH 7.6-7.8, whereas comammox (Nitrospira) nitrifiers and plant growth-promoting microbes were abundant in systems operating at pH 5.8-6.0. Lower pH systems supported more robust plant growth with no significant effects on fish health. This study demonstrated functional redundancy of aquaponics microbiota, with selectivity of nitrifying taxa as a function of pH. The results suggest that inoculum and pH are important considerations for aquaponics system initiation and optimization.

Longitudinal Survey of Aeromonas hydrophila and Foodborne Pathogens in a Commercial Aquaponics System

Aquaponic production of fresh produce is a sustainable agricultural method becoming widely adopted, though few studies have investigated potential food safety hazards within commercial systems. A longitudinal study was conducted to isolate and quantify several foodborne pathogens from a commercial, aquaponic farm, and to elucidate their distribution throughout. The survey was conducted over 2 years on a controlled-environment farm containing Nile tilapia (Oreochromis niloticus) and lettuce (Lactuca sativa). Samples (N = 1,047) were collected bimonthly from three identical, independent systems, and included lettuce leaves, roots, fingerlings (7-126 d old), feces from mature fish (>126 d old), water, and sponge swabs collected from the tank interior surface. Most probable number of generic Escherichia coli were determined using IDEXX Colilert Quanti-Tray. Enumeration and enrichment were used to detect Shiga toxin-producing E. coli (STEC), Salmonella enterica, Listeria monocytogenes, Aeromonas spp., Aeromonas hydrophilia, and Pseudomonas aeruginosa. Generic E. coli, STEC, L. monocytogenes, and S. enterica were not detected in collected samples. P. aeruginosa was isolated from water (7/351; 1.99%), swabs (3/351; 0.85%), feces (2/108; 1.85%), and lettuce leaves (2/99; 2.02%). A. hydrophila was isolated from all sample types (623/1047; 59.50%). The incidence of A. hydrophila in water (X2 = 23.234, p < 0.001) and sponge samples (X2 = 21.352, p < 0.001) increased over time.

Optimization of Plant Nutrition in Aquaponics: The Impact of Trichoderma harzianum and Bacillus mojavensis on Lettuce and Basil Yield and Mineral Status

The present study aims to test the effect of a nutrient solution, with the addition of microbial inoculum, on the growth and mineral composition of 'Hilbert' and 'Barlach' lettuce cultivars (Lactuca sativa var. crispa, L.) and basil (Ocimum basilicum, L.) cultivated in a vertical indoor farm. These crops were grown in four different variants of nutrient solution: (1) hydroponic; (2) aquaponic, derived from a recirculating aquaculture system (RAS) with rainbow trout; (3) aquaponic, treated with Trichoderma harzianum; (4) aquaponic, treated with Bacillus mojavensis. The benefits of T. harzianum inoculation were most evident in basil, where a significantly higher number of leaves (by 44.9%), a higher nitrate content (by 36.4%), and increased vitamin C (by 126.0%) were found when compared to the aquaponic variant. Inoculation with T. harzianum can be recommended for growing basil in N-limited conditions. B. mojavensis caused a higher degree of removal of Na+ and Cl- from the nutrient solution (243.1% and 254.4% higher, in comparison to the aquaponic solution). This is desirable in aquaponics as these ions may accumulate in the system solution. B. mojavensis further increased the number of leaves in all crops (by 44.9-82.9%) and the content of vitamin C in basil and 'Hilbert' lettuce (by 168.3 and 45.0%) compared to the aquaponic solution. The inoculums of both microbial species used did not significantly affect the crop yield or the activity of the biofilter. The nutrient levels in RAS-based nutrient solutions are mostly suboptimal or in a form that is unavailable to the plants; thus, their utilization must be maximized. These findings can help to reduce the required level of supplemental mineral fertilizers in aquaponics.

Microbiome study of a coupled aquaponic system: unveiling the independency of bacterial communities and their beneficial influences among different compartments

To understand the microbiome composition and interplay among bacterial communities in different compartments of a coupled freshwater aquaponics system growing flathead grey mullet (Mugil cephalus) and lettuces (Lactuca sativa), 16S rRNA gene amplicon sequencing of the V3-V4 region was analysed from each compartment (fish intestine, water from the sedimentation tank, bioballs from the biological filter, water and biofilm from the hydroponic unit, and lettuce roots). The bacterial communities of each sample group showed a stable diversity during all the trial, except for the fish gut microbiota, which displayed lower alpha diversity values. Regarding beta diversity, the structure of bacterial communities belonging to the biofilm adhering to the hydroponic tank walls, bioballs, and lettuce roots resembled each other (weighted and unweighted UniFrac distances), while bacteria from water samples also clustered together. However, both of the above-mentioned bacterial communities did not resemble those of fish gut. We found a low or almost null number of shared Amplicon Sequence Variants (ASVs) among sampled groups which indicated that each compartment worked as an independent microbiome. Regarding fish health and food safety, the microbiome profile did not reveal neither fish pathogens nor bacterial species potentially pathogenic for food health, highlighting the safety of this sustainable food production system.

Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes

Longitudinal sampling of the stool has yielded important insights into the ecological dynamics of the human gut microbiome. However, human stool samples are available approximately once per day, while commensal population doubling times are likely on the order of minutes-to-hours. Despite this mismatch in timescales, much of the prior work on human gut microbiome time series modeling has assumed that day-to-day fluctuations in taxon abundances are related to population growth or death rates, which is likely not the case. Here, we propose an alternative model of the human gut as a stationary system, where population dynamics occur internally and the bacterial population sizes measured in a bolus of stool represent a steady-state endpoint of these dynamics. We formalize this idea as stochastic logistic growth. We show how this model provides a path toward estimating the growth phases of gut bacterial populations in situ. We validate our model predictions using an in vitro Escherichia coli growth experiment. Finally, we show how this method can be applied to densely-sampled human stool metagenomic time series data. We discuss how these growth phase estimates may be used to better inform metabolic modeling in flow-through ecosystems, like animal guts or industrial bioreactors.

Gluconacetobacter diazotrophicus Inoculation of Two Lettuce Cultivars Affects Leaf and Root Growth under Hydroponic Conditions

The growth-promoting effects of Gluconacetobacter diazotrophicus inoculation on the leaf lettuce (Lactuca sativa L.) cultivars “Black Seeded Simpson” and “Bibb/Limestone” were investigated. Plants of each cultivar were grown hydroponically in Kratky jars in a growth chamber-controlled environment in a completely randomized factorial design with three or four replications. Each experiment was repeated once. Factors were (1) with or without inoculant and (2) seven levels of nitrogen (N) fertilization ranging from deficient (37.5 mg L−1 N) to excessive (172.5 mg L−1 N). The shoot, root, and total biomass accumulation, nitrogen density, and carbon/nitrogen (C/N) ratios were measured for each variety. Black Seeded Simpson demonstrated a shifting of production towards aerial tissues, with significantly greater shoot production and reduced root production. The observed increase in shoot biomass was greatest at the slightly deficient N rate of 105 mg L−1 N where inoculated plants produced 14.8% more than uninoculated plants. Lower N density and higher C/N ratios in inoculated shoot tissues indicate greater N use efficiency. Bibb/Limestone responded to inoculation with an average increase of 10.9% in shoot production and with greater root biomass. Bibb/Limestone also exhibited lower N density in inoculated shoot tissues with a corresponding increase in the C/N ratio. For growers looking to maximize lettuce yields, G. diaz inoculation may present a beneficial additive to the growing system by increasing leaf yields while not increasing N fertilizer requirements.

Development of an aquaponics microbial inoculum for efficient nitrification at acidic pH

Maintaining an optimal pH that simultaneously supports plants, fish, and nitrifying microorganisms is a challenge in recirculating aquaponics systems as nitrification is optimal at a slightly alkaline pH and plant growth is optimal at a slightly acidic pH. Freshwater fish tolerate pH > 5.5. Our aim was to adapt a microbial inoculum for a recirculating aquaponics system from an operational pH of 7.6 to 5.6, compare nitrification activity and production of N₂O, and describe changes in the adapted versus unadapted microbial communities. Four adaptation strategies were tested; our results indicated that a gradual reduction from pH 7.6 to 5.6, along with a gradual reduction followed by a gradual return of available ammonium, was the best strategy resulting in retention of 81% nitrification activity at pH 5.6 compared to pH 7.6. 16S rRNA gene amplicon sequencing and qPCR enumeration of nitrification-related genes showed that the composition of pH 5.6 adapted microbial communities from all four adaptation strategies was similar to one another and distinct from those operating at pH 7.6, with enrichment of comammox clade B bacteria over ammonia-oxidizing bacteria and thaumarchaeota. N₂O production of the pH 5.6 adapted microbial communities was below detection in all adaptation experiments, likely due to the increased proportion of comammox bacteria. Aquaponics biofilters enriched with comammox bacteria and adapted to function at pH 5.6 can be a desirable inoculum for freshwater recirculating aquaponics systems to retain nitrification activity and improve crop yields.Key points• Microbial communities adapted from pH 7.6 to pH 5.6 retained 81% nitrification activity.• Microbial communities adapted from pH 7.6 to pH 5.6 were enriched in comammox bacteria.• Comammox-enriched microbial communities did not produce N₂ O.