How to Manage and Identify Soil Mites & Other Problems
Dec 10, 2025
Soil-dwelling pests influence nearly every stage of production, from propagation through finishing. Because most activity occurs below the substrate surface, major problems often go unnoticed until crop growth becomes uneven, plants stall, or root systems collapse. Accurate soil pest diagnosis is essential for timing biological inputs, adjusting irrigation strategy, and protecting root-zone health. This guide outlines the key production pests encountered in substrate-based systems—primarily fungus gnats, shore flies, and root aphids—with practical identification methods and compatible biological control strategies.
1. Fungus Gnats: Root‑Feeding Larvae That Thrive Under High Moisture
Fungus gnat larvae remain the most impactful soil pest in propagation and vegetative production. UC IPM notes that Bradysia spp. larvae feed on decaying organic matter and algae but will also graze fine root hairs, young stems, and callus tissue as populations increase (UC IPM, 2020). These larvae require consistently moist substrate, and Oregon State University Extension reports that population growth accelerates rapidly under high moisture conditions and limited dry‑back (OSU Extension, 2018). Early signs include uneven growth across benches, delayed rooting of cuttings, and minor wilt or collapse despite adequate irrigation. Adults hover low over pots in a weak, mosquito‑like pattern and accumulate reliably on yellow sticky cards placed near the media surface (UC IPM, 2020). A potato‑slice larval check—pressing a thin slice onto the media for a few hours and then inspecting the underside—helps confirm larvae quickly at bench side (UC IPM, 2020).
For management, a coordinated program works best. Entonem (Steinernema feltiae) is the primary curative, applied as a drench to actively hunt larvae through the pore spaces of the media. Entomite‑M (Stratiolaelaps scimitus) complements this with steady, preventative pressure in the top half‑inch of substrate where eggs hatch and early instars feed. Where structural hotspots exist—wet bench edges, under benches, drain channels—adding Atheta (Dalotia coriaria) strengthens cleanup of exposed larval stages and intercepts pest stages along hardscape. Results improve markedly when moisture distribution and dry‑back are corrected, algae is removed, and low, lateral airflow is increased across the substrate surface (OSU Extension, 2018; UC IPM, 2020).
2. Shore Flies: Algae‑Driven Nuisance Pests That Indicate Moisture Excess
Shore flies (Scatella stagnalis) do not injure roots directly; they thrive where algae and standing water accumulate. According to UC IPM, larvae feed on algae and organic films at the surface, and adults are stockier than fungus gnats, with short, rapid flights and distinctive white spots on the wings that help confirm identification (UC IPM, 2020). Heavy populations splash contaminants onto foliage and surfaces and are especially common in ebb‑and‑flow and hydroponic systems where algae films form on trays, floors, and drains.
Primary control is environmental. Production wins come from increasing surface dry‑back, eliminating standing water, fixing drain slow‑downs, scrubbing algae, and improving low‑level airflow (UC IPM, 2020). Biologically, Atheta can contribute at the margins by feeding on exposed shore fly stages in wet structural zones, but it should be considered supportive rather than standalone. While Steinernema feltiae can contact larvae under certain conditions, shore‑fly suppression remains inconsistent if algae pressure is not addressed. In practice, growers get durable results by treating shore flies as an algae and moisture problem first, then letting the fungus‑gnat program (Entonem + Entomite‑M, with Atheta in structural hotspots) mop up shared conditions that otherwise sustain both flies (UC IPM, 2020).
3. Root Aphids: Hidden, Colony‑Forming Pests That Disrupt Growth Uniformity
Root aphids are difficult to diagnose because they feed below the media surface and mimic nutrition or irrigation problems. UC IPM notes that aphids feeding on roots and lower stems cause patchy chlorosis, stunting, wilt in normal irrigation windows, and local collapse (UC IPM, 2021). A white, waxy residue on roots or at the crown, together with persistent ant activity, is a strong diagnostic signal because ants protect colonies in exchange for underground honeydew (RHS, 2020). Winged forms may appear under crowding or stress, but sticky cards often miss established subterranean populations (UC IPM, 2021).
Below the media line, no single predator eradicates root aphids, so practical control focuses on control through microbial and chemical. An Isarid dip or drench (Isaria fumosorosea) combined with a neem‑based concentrate (azadirachtin) is effective at managing root aphids. Dips are well‑suited to young plants and transplants; drenches/"sprenches" (spray+drench) fit established plants. Apply in low light with good humidity, ensure thorough wetting around crowns and root balls, and repeat on a short interval to align with aphid reproduction. Pair treatments with ant suppression and tight sanitation to remove colony protection and prevent spread (UC IPM, 2021; RHS, 2020). If above‑ground aphids appear on stems or leaves, you can overlay Aphidius parasitoids or Aphidoletes for those exposed stages; treat this as topside control while the Isarid + neem program targets the root‑zone component. Cultural corrections—firmer irrigation discipline for better oxygenation, tidier propagation blocks, and clean media handling—are decisive in whether pressure fades or flares (UC IPM, 2021).
4. Soil Mites: Common, Often Beneficial Organisms in Active Substrates
Soil mites are present in nearly every greenhouse substrate and are frequently beneficial. University of Maryland Extension highlights that many soil‑inhabiting mites prey on fungus gnat larvae, thrips pupae, and other micro‑arthropods or function as decomposers that recycle organic matter (UMD Extension, 2020). When growers notice more mites in saturated or decomposing media, it is typically a signal of conditions that also elevate fungus gnats and microbes, not a pest outbreak caused by the mites themselves. Do not treat beneficial soil mites; instead, improve aeration and dry‑back, rebalance media where decomposition is high, and correct watering or drainage. Inputs like Entomite‑M complement the beneficial predator community rather than displacing it (UMD Extension, 2020).
5. Springtails: Moisture‑Level Indicators, Not Production Pests
Springtails (Collembola) become visible when substrate moisture stays high, especially in propagation. RHS notes that they feed on fungi and organic debris rather than living plant tissue (RHS, 2020). Springtails signal a moisture and algae environment that favors true root‑zone pests like fungus gnats, but springtails themselves are not a production pest and do not warrant treatment. As irrigation normalizes and surfaces dry, springtail counts decline without intervention.
6. Soil Mealybugs: Root‑Zone Colonizers That Hide in Wax and Fiber
Soil mealybugs establish in and around the root zone, often inside pot crevices, at the crown, and along drainage holes. Colonies are concealed by white, cottony wax and can persist for weeks before the crop shows obvious symptoms. Early indicators include uneven growth, poor vigor despite normal irrigation, pale or patchy chlorosis, and occasional ant activity at the pot line. Unlike above‑ground mealybugs, honeydew may be less obvious in the soil environment, so the most reliable signs are cottony deposits around roots and crown tissue, slow recovery after watering, and small clusters that cling to pot walls or roots when plants are lifted for inspection (RHS, 2020).
Accurate diagnosis starts with a careful check of the crown and root ball. Lift a few representative plants, loosen the media gently, and look for cottony masses and soft, pale insects grouped along fibrous roots or in protected niches. Inspect the outside of pots and the drainage holes because infestations frequently anchor there and spread to adjacent containers. Sticky cards are not helpful for detection; mapping symptoms and ant trails will guide you more effectively to the hotspots. If colonies are present, treat the issue as a container‑level problem first and a bench‑level problem second, because movement of infested pots and media is the fastest route of spread (RHS, 2020).
Management in the root zone responds best to targeted dips or drenches plus strict sanitation. In our program, an Isarid dip or drench (Isaria fumosorosea) combined with a neem‑based concentrate (azadirachtin) is effective in managing soil mealybugs. Dips suit young plants and transplants; drenches suit established containers. Apply in low light with supportive humidity, thoroughly wet the crown, root ball, pot exterior, and the immediate bench surface, and repeat on a short interval to keep pace with mealybug reproduction.
References
UC Statewide Integrated Pest Management Program (UC IPM). “Fungus Gnats.” 2020.
UC Statewide Integrated Pest Management Program (UC IPM). “Shore Flies in Greenhouses.” 2020.
UC Statewide Integrated Pest Management Program (UC IPM). “Aphids: Management and Diagnosis.” 2021.
Oregon State University Extension. “Fungus Gnats in Greenhouses.” 2018.
Royal Horticultural Society (RHS). “Sap‑feeding insects.” 2020.
University of Maryland Extension. “Mites in Home Gardens.” 2020.
