Impact of Peat Mining and Restoration on Methane Turnover Potential and Methane-Cycling Microorganisms in a Northern Bog.

Ombrotrophic peatlands are a recognized global carbon reservoir. Without restoration and peat regrowth, harvested peatlands are dramatically altered, impairing their carbon sink function, with consequences for methane turnover. Previous studies determined the impact of commercial mining on the physicochemical properties of peat and the effects on methane turnover. However, the response of the underlying microbial communities catalyzing methane production and oxidation have so far received little attention. We hypothesize that with the return of Sphagnum spp. postharvest, methane turnover potential and the corresponding microbial communities will converge in a natural and restored peatland. To address our hypothesis, we determined the potential methane production and oxidation rates in natural (as a reference), actively mined, abandoned, and restored peatlands over two consecutive years. In all sites, the methanogenic and methanotrophic population sizes were enumerated using quantitative PCR (qPCR) assays targeting the mcrA and pmoA genes, respectively. Shifts in the community composition were determined using Illumina MiSeq sequencing of the mcrA gene and a pmoA-based terminal restriction fragment length polymorphism (t-RFLP) analysis, complemented by cloning and sequence analysis of the mmoX gene. Peat mining adversely affected methane turnover potential, but the rates recovered in the restored site. The recovery in potential activity was reflected in the methanogenic and methanotrophic abundances. However, the microbial community composition was altered, being more pronounced for the methanotrophs. Overall, we observed a lag between the recovery of the methanogenic/methanotrophic activity and the return of the corresponding microbial communities, suggesting that a longer duration (>15 years) is needed to reverse mining-induced effects on the methane-cycling microbial communities.IMPORTANCE Ombrotrophic peatlands are a crucial carbon sink, but this environment is also a source of methane, an important greenhouse gas. Methane emission in peatlands is regulated by methane production and oxidation catalyzed by methanogens and methanotrophs, respectively. Methane-cycling microbial communities have been documented in natural peatlands. However, less is known of their response to peat mining and of the recovery of the community after restoration. Mining exerts an adverse impact on potential methane production and oxidation rates and on methanogenic and methanotrophic population abundances. Peat mining also induced a shift in the methane-cycling microbial community composition. Nevertheless, with the return of Sphagnum spp. in the restored site after 15 years, methanogenic and methanotrophic activity and population abundance recovered well. The recovery, however, was not fully reflected in the community composition, suggesting that >15 years are needed to reverse mining-induced effects.

Aerobes and phototrophs as microbial organic fertilizers: Exploring mineralization, fertilization and plant protection features.

Organic fertilizers and especially microbial biomass, also known as microbial fertilizer, can enable a paradigm shift to the conventional fertilizer-to-food chain, particularly when produced on secondary resources. Microbial fertilizers are already common practice (e.g. Bloom® and Synagro); yet microbial fertilizer blends to align the nutrient release profile to the plant's needs are, thus far, unexplored. Moreover, most research only focuses on direct fertilization effects without considering added value properties, such as disease prevention. This study has explored three promising types of microbial fertilizers, namely dried biomass from a consortium of aerobic heterotrophic bacteria, a microalga (Arthrospira platensis) and a purple non-sulfur bacterium (Rhodobacter sphaeroides). Mineralization and nitrification experiments showed that the nitrogen mineralization profile can be tuned to the plant's needs by blending microbial fertilizers, without having toxic ammonium peaks. In a pot trial with perennial ryegrass (Lolium perenne L.), the performance of microbial fertilizers was similar to the reference organic fertilizer, with cumulative dry matter yields of 5.6-6.7 g per pot. This was confirmed in a pot trial with tomato (Solanum lycopersicum L.), showing an average total plant length of 90-99 cm after a growing period of 62 days for the reference organic fertilizer and the microbial fertilizers. Moreover, tomato plants artificially infected with powdery mildew (Oidium neolycopersici), a devastating disease for the horticultural industry, showed reduced disease symptoms when A. platensis was present in the growing medium. These findings strengthen the application potential of this novel class of organic fertilizers in the bioeconomy, with a promising match between nutrient mineralization and plant requirements as well as added value in crop protection.

In-Depth Observation on the Microbial and Fungal Community Structure of Four Contrasting Tomato Cultivation Systems in Soil Based and Soilless Culture Systems.

As soil and soilless culture systems are highly dynamic environments, the structure of rhizosphere microbial communities is consistently adapting. There is a knowledge gap between the microbial community structure of soil based and soilless culture systems and thus we aimed at surveying their impact on diversity and composition of bacterial communities across a 10-month period in a tomato cultivation system. We compared community metrics between an soil based culture system fertilized with malt sprouts and blood meal, known for its slow and high mineralization rate, respectively and a soilless culture system fertilized with fish effluent or supplemented with an liquid organic fertilizer. Bacterial and fungal community composition was followed over time using two complementary techniques, phospholipid fatty acid analysis and 16S rRNA amplicon sequencing. Nitrogen dynamics and plant performance were assessed to provide insight on how bacterial diversity of soil and soilless microbial communities ultimately impacts productivity. Similar plant performance was observed in soilless culture systems and soil based system and yield was the highest with the aquaponics-derived fertilizer. Soil and soilless cultivating systems supplemented with different nitrogen-rich fertilizers differed on its characteristics throughout the experimental period. Fast-paced fluctuations in pH(H2O) and nutrient cycling processes were observed in growing medium. Physicochemical characteristics changed over time and interacted with bacterial community metrics. Multivariate analysis showed that plant length, pH, Flavisolibacter, phosphorus, chloride, ammonium, potassium, calcium, magnesium, sodium, electrical conductivity, nitrate, sulfate, and the bacterial genera Desulfotomaculum, Solirubrobacter, Dehalococcoides, Bythopirellula, Steroidobacter, Litorilinea, Nonomuraea were the most significant factors discriminating between natural soils supplemented with animal and plant by-products. Long-term fertilizer regimes significantly changed the PLFA fingerprints in both the soilless culture and soil based culture system. The use of these by-products in the soil was positively associated with arbuscular mycorrhizal fungi (AMF), which may influence rhizosphere communities through root exudates and C translocation. Community structure was distinct and consistently different over time, despite the fertilizer supplementation. The fungal microbial community composition was less affected by pH, while the composition of the bacterial communities (Actinomycetes, Gram-negative bacteria, and Gram-positive bacteria) was closely defined by soil pH, demonstrating the significance of pH as driver of bacterial community composition. Fertilizer application may be responsible for variations over time in the ecosystem. Knowledge about the microbial interactions in tomato cultivating systems opens a window of opportunity for designing targeted fertilizers supporting sustainable crop production.

Effect of Applying Struvite and Organic N as Recovered Fertilizers on the Rhizosphere Dynamics and Cultivation of Lupine (Lupinus angustifolius).

Intensive agriculture and horticulture heavily rely on the input of fertilizers to sustain food (and feed) production. However, high carbon footprint and pollution are associated with the mining processes of P and K, and the artificial nitrogen fixation for the production of synthetic fertilizers. Organic fertilizers or recovered nutrients from different waste sources can be used to reduce the environmental impact of fertilizers. We tested two recovered nutrients with slow-release patterns as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as a nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in lupine plants. Plant performance was not affected by the fertilizer applied; however, N recovery was higher from the organic fertilizer than from struvite. As root architecture is fundamental for plant productivity, variations in root structure and length as a result of soil nutrient availability driven by plant-bacteria interactions were compared showing also no differences between fertilizers. However, fertilized plants were considerably different in the root length and morphology compared with the no fertilized plants. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed that the fertilizer applied had a significant impact on the associations and functionality of the bacteria inhabiting the growing medium used. The type of fertilizer significantly influenced the interindividual dissimilarities in the most abundant genera between treatments. This means that different plant species have a distinct effect on modulating the associated microbial community, but in the case of lupine, the fertilizer had a bigger effect than the plant itself. These novel insights on interactions between recovered fertilizers, plant, and associated microbes can contribute to developing sustainable crop production systems.

Purple non-sulphur bacteria and plant production: benefits for fertilization, stress resistance and the environment.

Purple non-sulphur bacteria (PNSB) are phototrophic microorganisms, which increasingly gain attention in plant production due to their ability to produce and accumulate high-value compounds that are beneficial for plant growth. Remarkable features of PNSB include the accumulation of polyphosphate, the production of pigments and vitamins and the production of plant growth-promoting substances (PGPSs). Scattered case studies on the application of PNSB for plant cultivation have been reported for decades, yet a comprehensive overview is lacking. This review highlights the potential of using PNSB in plant production, with emphasis on three key performance indicators (KPIs): fertilization, resistance to stress (biotic and abiotic) and environmental benefits. PNSB have the potential to enhance plant growth performance, increase the yield and quality of edible plant biomass, boost the resistance to environmental stresses, bioremediate heavy metals and mitigate greenhouse gas emissions. Here, the mechanisms responsible for these attributes are discussed. A distinction is made between the use of living and dead PNSB cells, where critical interpretation of existing literature revealed the better performance of living cells. Finally, this review presents research gaps that remain yet to be elucidated and proposes a roadmap for future research and implementation paving the way for a more sustainable crop production.

Storage, fertilization and cost properties highlight the potential of dried microbial biomass as organic fertilizer.

The transition to sustainable agriculture and horticulture is a societal challenge of global importance. Fertilization with a minimum impact on the environment can facilitate this. Organic fertilizers can play an important role, given their typical release pattern and production through resource recovery. Microbial fertilizers (MFs) constitute an emerging class of organic fertilizers and consist of dried microbial biomass, for instance produced on effluents from the food and beverage industry. In this study, three groups of organisms were tested as MFs: a high-rate consortium aerobic bacteria (CAB), the microalga Arthrospira platensis ('Spirulina') and a purple non-sulfur bacterium (PNSB) Rhodobacter sp. During storage as dry products, the MFs showed light hygroscopic activity, but the mineral and organic fractions remained stable over a storage period of 91 days. For biological tests, a reference organic fertilizer (ROF) was used as positive control, and a commercial organic growing medium (GM) as substrate. The mineralization patterns without and with plants were similar for all MFs and ROF, with more than 70% of the organic nitrogen mineralized in 77 days. In a first fertilization trial with parsley, all MFs showed equal performance compared to ROF, and the plant fresh weight was even higher with CAB fertilization. CAB was subsequently used in a follow-up trial with petunia and resulted in elevated plant height, comparable chlorophyll content and a higher amount of flowers compared to ROF. Finally, a cost estimation for packed GM with supplemented fertilizer indicated that CAB and a blend of CAB/PNSB (85%/15%) were most cost competitive, with an increase of 6% and 7% in cost compared to ROF. In conclusion, as bio-based fertilizers, MFs have the potential to contribute to sustainable plant nutrition, performing as good as a commercially available organic fertilizer, and to a circular economy.

Tomato plants rather than fertilizers drive microbial community structure in horticultural growing media.

Synthetic fertilizer production is associated with a high environmental footprint, as compounds typically dissolve rapidly leaching emissions to the atmosphere or surface waters. We tested two recovered nutrients with slower release patterns, as promising alternatives for synthetic fertilizers: struvite and a commercially available organic fertilizer. Using these fertilizers as nitrogen source, we conducted a rhizotron experiment to test their effect on plant performance and nutrient recovery in juvenile tomato plants. Plant performance was significantly improved when organic fertilizer was provided, promoting higher shoot biomass. Since the microbial community influences plant nitrogen availability, we characterized the root-associated microbial community structure and functionality. Analyses revealed distinct root microbial community structure when different fertilizers were supplied. However, plant presence significantly increased the similarity of the microbial community over time, regardless of fertilization. Additionally, the presence of the plant significantly reduced the potential ammonia oxidation rates, implying a possible role of the rhizosheath microbiome or nitrification inhibition by the plant. Our results indicate that nitrifying community members are impacted by the type of fertilizer used, while tomato plants influenced the potential ammonia-oxidizing activity of nitrogen-related rhizospheric microbial communities. These novel insights on interactions between recovered fertilizers, plant and associated microbes can contribute to develop sustainable crop production systems.

Growing media constituents determine the microbial nitrogen conversions in organic growing media for horticulture.

Vegetables and fruits are an important part of a healthy food diet, however, the eco-sustainability of the production of these can still be significantly improved. European farmers and consumers spend an estimated €15.5 billion per year on inorganic fertilizers and the production of N-fertilizers results in a high carbon footprint. We investigated if fertilizer type and medium constituents determine microbial nitrogen conversions in organic growing media and can be used as a next step towards a more sustainable horticulture. We demonstrated that growing media constituents showed differences in urea hydrolysis, ammonia and nitrite oxidation and in carbon dioxide respiration rate. Interestingly, mixing of the growing media constituents resulted in a stimulation of the function of the microorganisms. The use of organic fertilizer resulted in an increase in amoA gene copy number by factor 100 compared to inorganic fertilizers. Our results support our hypothesis that the activity of the functional microbial community with respect to nitrogen turnover in an organic growing medium can be improved by selecting and mixing the appropriate growing media components with each other. These findings contribute to the understanding of the functional microbial community in growing media and its potential role towards a more responsible horticulture.

Mineral and organic growing media have distinct community structure, stability and functionality in soilless culture systems.

The choice of soilless growing medium for plant nutrition, growth and support is crucial for improving the eco-sustainability of the production in horticultural systems. As our current understanding of the functional microbial communities inhabiting this ecosystem is still limited, we examined the microbial community development of the two most important growing media (organic and mineral) used in open soilless horticultural systems. We aimed to identify factors that influence community composition over time, and to compare the distribution of individual taxa across growing media, and their potential functionality. High throughput sequencing analysis revealed a distinctive and stable microbial community in the organic growing medium. Humidity, pH, nitrate-N, ammonium-N and conductivity were uncovered as the main factors associated with the resident bacterial communities. Ammonium-N was correlated with Rhizobiaceae abundance, while potential competitive interactions among both Methylophilaceae and Actinobacteridae with Rhizobiaceae were suggested. Our results revealed that soilless growing media are unique niches for diverse bacterial communities with temporal functional stability, which may possibly impact the resistance to external forces. These differences in communities can be used to develop strategies to move towards a sustainable horticulture with increased productivity and quality.