Biology subjects

Niemi, J.

Publications and source records attributed to Niemi, J..

8 recordsLinked to original sources

bioRxiv2026

Operationalising the context in regenerative agriculture: decision-making and farm variability

Soil degradation is a widespread challenge that requires a broad response at the individual farm level. To ensure effectivity, the practices should be tailored to the farm context: land manager objectives and farm specific challenges. These have however been difficult to quantify. Here we demonstrate that a workable farm context can be created based on a value survey, open satellite and soil data, and published models for vegetation gross primary productivity and soil erosion. Based on the findings, despite individual differences, farmers value profitability and operational efficiency, but also biodiversity and soil health. At least the regenerative farmers surveyed also value working for the greater good more than maintaining tradition or power. In spite of wide differences in farm production orientation, we also found that each farm also had a broad variation in individual fields GPP. Most fields have a stable GPP level, which is either high or low, and that there is a 2-3-fold difference between the weakest and best producing fields indicating the potential for improving GPP by improving the growing conditions on currently weak fields. In addition, soil loss was found to be highly concentrated in critical source areas, where 10% of the field area contributed to 50% of the soil loss. Overall, open data can be linked to modelling workflows to rapidly produce a decision-making context for farmers. This facilitates benchmarking and co-learning as well as enables land managers and advisors to identify the farm context for planning effective responses to soil degradation.

ecology↗

bioRxiv2025

Targeting phosphorus loss with carbon farming practices? Results from an on-farm study

Agricultural soils lose P to waterbodies and C to the atmosphere. Reversing the C trend requires change in management (carbon farming), but what is the effect of carbon farming practices on P transport from soils to waterbodies? This was empirically studied by analyzing the P loss risks from 20 farms participating in a 5-year on-farm carbon farming experiment. We evaluated the effect of C farming practices on soil P balance, P stocks, and potential P loss through surface and subsurface runoff and erosion. Based on the results, carbon farming had only minor impacts on P loss compared with the current soil conservation practices already applied by the farms. The farmers did not utilize the opportunity to reduce P fertilization through some carbon farming practices which could improve soil P availability, therefore resulting in weak P balances. Furthermore, only a small fraction of the field area (18%) was responsible for the majority (50%) of the estimated P loss, indicating the importance of P loss hotspots. C farming practices do not seem to improve water quality unless they are tailored to target key processes of P loss such as maintaining a negative P balance on high-P sites, reducing runoff, and focusing on local critical source areas.

ecology↗

bioRxiv2025

Teaching good agronomic practices to strengthen pigeon pea cultivation and value chains through farmer-to-farmer education in Zambia

Farmer field schools (FFSs) are transformative, participatory approaches to adult agricultural education that effectively promote farmers learning and capacity building and empower farming communities with practical knowledge. Here, we present a case study of FFS in the Katete district, Eastern province of Zambia, focused on good pigeon pea agronomic practices and the value chain. Three FFSs were established, focusing on a variety of trials, bio-pesticides, and a pigeon pea-specific rhizobial inoculant. Extreme weather conditions, an underdeveloped pigeon pea seed value chain, and a poor seed system hindered the implementation of the FFSs. To strengthen the pigeon pea seed value chain, a seed dehuller is now available to farmers. Our results highlight the importance of the design, implementation, monitoring, and evaluation of the FFSs. Pigeon pea FFSs will support crop and food diversification, improve soil fertility and sustainable agriculture, and may increase household income.

scientific communication and education↗

bioRxiv2024

Brain tumor induce immunoregulatory dendritic cells in tumor draining lymph nodes that can be targeted by OX40

Brain tumors and metastases have a poor prognosis due to the unique characteristics of the central nervous system (CNS) and tumor immune microenvironment (TIME). CNS tumors exhibit limited infiltration and activation of dendritic cells (DCs) in tumor tissue and tumor-draining lymph nodes (TdLN), which regulate immune responses influenced by factors in the TIME. The immune response in the brain is significantly different from the rest of the body, and although DC subtypes have been identified in mice and humans with brain tumors or metastases, little is known how they affect the response to immunotherapy. We investigated the immunoregulatory function of cervical DCs (DC-c) compared to peripheral DCs (DC-p) in TdLN. Our analysis revealed that DC-c have unique phenotypes and promoted regulatory T cell expansion and poorly cytotoxic CD8 T cells compared to DC-p. Furthermore, we identified OX40 as a modulator of immunoregulatory DC-c function, and Batf3 knockout confirmed the essential role of DC-c in mounting an immune response to brain tumors. Additionally, the expression of markers associated with mature regulatory DCs (mregDC) in TdLN was associated with immune regulation in the CNS and the response to OX40. Our findings highlight that immunotherapy interventions can modulate DC-cs immunoregulatory function, offering an innovative approach for optimized immunotherapy against CNS malignancies.

immunology↗

bioRxiv2023

Breeding for growth has resulted in increased tolerance to drought at the cost of genetic diversity in Scots pine.

Climate change possess a threat to forests and forestry. Drought has been identified as a one of the main issues due to its interaction with other biotic and abiotic stresses. Few studies have been done regarding breeding effect on the adaptability to climate change. After a common garden experiment with seedling families of Scots pine from northern Sweden, we have found differences in drought tolerance between families of breeding and natural origin. We performed a high throughput analysis-based phenotyping on both canopy and root traits. Root architecture traits might be related to drought tolerance and show moderate to high heritability values. The heritability of root architecture traits can be useful not only for drought but also for adaptability to other abiotic stresses. Analysis on architecture traits show that, especially on canopy-traits, families from breeding origins show less phenotypic variance than the ones from natural origins. The methodology employed to evaluate drought tolerance and plant architecture might be useful for future research and forest management focused on climate change adaptability.

physiology↗

bioRxiv2023

Physical interactions trigger Streptomyces to prey on yeast using natural products and lytic enzymes

Microbial predators obtain energy from killing other living cells. In this study, we present compelling evidence demonstrating that widely distributed Streptomyces soil bacteria, typically not considered as predators, possess the ability to detect and prey on Saccharomyces cerevisiae. Using fluorescence microscopy, we observed that predation is initiated by physical contact between Streptomyces lavendulae YAKB-15 and yeast cells. Comparative transcriptomics data indicated that the interaction triggered the production of numerous lytic enzymes to digest all major components of the yeast cell wall. The production of various glucanases, mannosidases and chitinases was confirmed by proteomics and enzymatic activity measurements. In order to destabilise the yeast cell membrane and assimilate yeast, Streptomyces lavendulae YAKB-15 induced production of cell-associated antifungal polyenes, namely pentamycin and filipin III, and cholesterol oxidase ChoD. In response, yeast downregulated protein synthesis and attempted to enter a quiescence-like state. We show that yeast predation is a common phenomenon in Streptomyces, including well-characterized strains such as Streptomyces peucetius ATCC 27952, where the interaction led to production of 14-hydroxyisochainin. Finally, gene inactivation studies lead us to propose a multidirectional assault model harbouring numerous redundancies that are not dependant on any single individual factor. Our results provide insights into the ecological role of Streptomyces and highlight the utilization of predation as a mechanism to elicit the production of bioactive natural products for drug discovery. Significance StatementSoil is a rich environment for microbes, where they compete for space and resources. Streptomyces bacteria are well-known for their ability to synthesize natural products, particularly antibiotics, that are used in chemical defense against competing microbes. Here we show that Streptomyces are, in fact, predatory bacteria. Upon encountering yeast cells, Streptomyces initiate the production of numerous enzymes that digest the cell wall of yeast. In addition, the interaction triggers the production of natural products that destabilize the yeast cell membrane. Collectively these actions lead to the death of yeast cells and release of cellular building blocks that Streptomyces can use as nutrients. The work fundamentally shifts the paradigm of how Streptomyces are perceived within the soil microbiome ecosystem.

microbiology↗

bioRxiv2022

Subsensory stochastic electrical stimulation targeting muscle afferents alters gait control during locomotor adaptations to haptic perturbations

Subsensory noise stimulation targeting sensory receptors has been shown to improve balance control in healthy and impaired individuals. However, the potential for application of this technique in other contexts is still unknown. Gait control and adaptation rely heavily on the input from proprioceptive organs in the muscles and joints. Here we investigated the use of subsensory noise stimulation as a means to influence motor control by "boosting" proprioception during locomotor adaptations to forces delivered by a robot. The forces increase step length unilaterally and trigger an adaptive response that restores the original symmetry. Healthy participants performed two adaptation experiments, one with stimulation applied to the hamstring muscles and one without. We found that participants adapted faster but to a lesser extent when undergoing subsensory stimulation. We argue that this behaviour is due to the dual effect that the stimulation has on the afferents encoding position and velocity that are present in the muscle spindles.

neuroscience↗

bioRxiv2021

Evolution-Inspired Engineering of Anthracycline Methyltransferases

Streptomyces soil bacteria produce hundreds of anthracycline anticancer agents with a relatively conserved set of genes. This diversity depends on the rapid evolution of biosynthetic enzymes to acquire novel functionalities. Previous work has identified S-adenosyl-L-methionine-dependent methyltransferase-like proteins that catalyze either 4-O-methylation, 10-decarboxylation or 10-hydroxylation, with additional differences in substrate specificities. Here we focused on four protein regions to generate chimeric enzymes using sequences from four distinct subfamilies to elucidate their influence in catalysis. Combined with structural studies we managed to depict factors that influence gain-of-hydroxylation, loss-of-methylation and substrate selection. The engineering expanded the catalytic repertoire to include novel 9,10-elimination activity, and 4-O-methylation and 10-decarboxylation of unnatural substrates. The work provides an instructive account on how the rise of diversity of microbial natural products may occur through subtle changes in biosynthetic enzymes.

biochemistry↗