Manure management glossary

Plain definitions for the terms used across manure pit and lagoon management — the gases, the bacteria, the structures, and the nutrient chemistry. Written for operators, not for a textbook.

Aerobic bacteria: Bacteria that need free oxygen to live and work. In a manure pit they only survive near the surface or wherever agitation folds air into the liquid, so they do little of the work down deep. They digest fast when they have air, which is why some operations aerate their storage. Below the crust, oxygen runs out within an inch or two and the anaerobic bacteria take over.
Agitation: Stirring stored manure with a prop or a recirculating pump so the solids go back into suspension before pumping. It is the most dangerous routine job on the place, because it releases hydrogen sulfide and methane fast and the gas comes up through the slats into the barn. Ventilate at full rate, get people and animals clear where you can, and never enter the pit. The more crust and hardpan you have built up, the longer you have to agitate.
Ammonia (NH3): A sharp-smelling nitrogen gas released as bacteria break down protein and urea in manure. It is lighter than air, it irritates the eyes and airways of both people and livestock, and every pound that leaves the pit is fertilizer value you paid for and did not get. In liquid manure it sits in balance with ammonium; warmer and more alkaline conditions push more of it into the air.
Ammonium nitrogen: The dissolved, plant-available nitrogen in liquid manure, listed as NH4-N on a manure test. It behaves much like the nitrogen in commercial fertilizer, which is why it gets close to full credit in a nutrient plan. It also converts to ammonia gas and leaves in a hurry if manure lies on the surface, so injection or quick incorporation is how you keep it.
Anaerobic digestion: The breakdown of manure solids by bacteria working without oxygen. It happens in every covered pit and every lagoon whether you plan for it or not. It runs in stages: one group of bacteria breaks complex solids into sugars and acids, and a slower group converts those acids into methane and carbon dioxide. When the acid stage runs ahead of the methane stage, the pit sours, gas production falls off, and solids start stacking up.
Bioaugmentation: Bioaugmentation is the addition of selected bacteria to help a manure system break down material that the existing bacterial population is not handling effectively. Some PitCharger products use bacteria; others work through other specific modes of action, so not every PitCharger product falls into this category.
CAFO (Concentrated Animal Feeding Operation): A regulatory classification under the Clean Water Act for operations that confine animals above set head counts and do not grow crops or forage in the confinement area. Operations that meet the large thresholds generally need a discharge permit, a nutrient management plan, and records of manure application and storage inspections. Most of the permitting is handled by state agencies, and the head-count thresholds differ by species.
Cellulose: The main structural fiber in plant cell walls, and the bulk of what passes through a hog or a steer undigested. Corn hulls, cob, stalk, and bedding all come into the pit as cellulose. It digests slowly, and most pits do not carry enough fiber-degrading bacteria to keep up with what comes in. That backlog is what builds crust on top and packs solids on the bottom.
Corn pith: The soft, spongy tissue inside the corn stalk and cob. It comes into a pit with bedding and with what passes through the animal, and it soaks up liquid and floats. Pith is mostly cellulose wrapped in lignin, so it digests slowly and tends to end up in the crust instead of breaking down. Operations feeding a lot of high-fiber byproduct see more of it come through.
Crust: The mat of floating fiber, hair, and bedding that forms on top of stored manure, held up by gas bubbles rising underneath. A thin crust on outside storage is useful, since it cuts ammonia loss and holds down odor. A thick, hard crust is a different matter: it traps gas beneath it, takes hours of agitation to break up, and tells you fiber is coming in faster than the bacteria are breaking it down.
Deep pit: A manure storage built directly under the slatted floor of the barn, commonly eight to ten feet deep, holding manure for six months to a year between pumpings. Everything the animals produce drops straight in and sits there with no oxygen for a long stretch. Because of that holding time, deep pits build the heaviest crust and the most settled solids, and they hold the most gas under the slats.
Earthen lagoon: An outdoor clay-lined basin used to store and partly treat liquid manure. Solids settle to the bottom as sludge, liquid stays in the middle, and a crust usually forms across the top. Treatment slows way down in cold weather, so through the winter a lagoon is mostly storing rather than digesting. Sludge depth has to be tracked, because it takes away storage capacity a foot at a time.
Facultative bacteria: Facultative bacteria can function with or without oxygen, which allows them to remain active as conditions change within a manure pit or lagoon. Oxygen is present at the surface and gone a few inches down, and conditions swing again with agitation, pumping, cold snaps, and refill.
Freeboard: The empty space between the manure surface and the top of the storage, measured in feet. It is your margin for rainfall, snowmelt, and the stretches when you cannot get on the field. Permits and nutrient management plans set a minimum you have to keep, and inspectors check it. Settled solids cut into that margin from the bottom even in a year when you have not added a thing.
Hardpan: The dense, packed layer of settled solids on the floor of a pit or lagoon that will not go back into suspension with normal agitation. It builds out of sand, grit, feed fines, and undigested fiber the bacteria never got through. Hardpan takes storage capacity away for good until it is broken up or scraped out. It is the reason a pit that once held a year of manure now fills up in eight or nine months.
Hydrogen sulfide (H2S): A toxic gas produced when bacteria break down sulfur compounds in manure without oxygen. It is heavier than air, so it settles down in the pit and stays there until something stirs the manure. Low concentrations smell like rotten eggs, but higher concentrations deaden the sense of smell within a minute or two, so the warning disappears while the danger climbs. That olfactory fatigue is a large part of why it kills people during agitation and pumping.
Lignin: The woody compound that stiffens plant cell walls and locks cellulose inside them. Bacteria break lignin down very slowly, and under the low-oxygen conditions in a manure pit, close to not at all. Whatever lignin comes in with cob, stalk, and bedding mostly stays put, and it protects the fiber bound up with it. Over time it settles out and becomes part of the material you have to agitate hard or scrape out.
Manure pit foam: A thick, stable layer of bubbles that builds on stored swine manure, sometimes several feet deep under the slats. The bubbles are wrapped in fiber and biofilm, and they hold methane at high concentration instead of letting it vent off. That is what makes foam dangerous: agitation, a spark, or a heater pilot can release all that gas at once, and barns have been lost to flash fires because of it. Foam generally shows up where digestion is out of balance.
Methane (CH4): The main flammable gas that comes off anaerobic digestion of manure. It has no odor of its own and it is lighter than air, so it collects under slats, in headspace, and in bubbles trapped in foam. Methane is explosive in air at roughly 5 to 15 percent by volume. That is why a spark, a torch, or a heater pilot over a foaming pit has set off flash fires in hog barns.
Mineralization: The conversion of organic nitrogen in manure into plant-available ammonium by soil microbes. It runs on warmth and moisture, so most of it happens through the growing season and stalls out when the ground is cold. Only part of the organic nitrogen you apply mineralizes the first year; the rest carries over and feeds later crops. That carryover is why manured ground keeps producing after the year it was applied.
Nutrient management plan: The written plan that lays out how much manure you can apply, where, and when, based on soil tests, manure tests, crop removal, and setbacks from wells and waterways. Permitted operations are required to have one and to keep records showing they followed it. It is built around nitrogen and phosphorus, and it drives your application rates, how many acres you need, and how much storage you have to keep open.
Organic nitrogen: Nitrogen still bound up in proteins and solids in manure, not yet in a form a plant can take up. Soil microbes have to break it down first, so it releases over a season and beyond rather than all at once. Manure tests report it separately from ammonium for that reason. Crediting it correctly, including the carryover into later years, is part of any nutrient plan.
Pull plug system: A shallow under-barn pit with a standpipe or plug that gets pulled every week or two to drain manure to an outside storage. Keeping the pit shallow cuts gas exposure in the barn and moves manure out while it is still fresh. The catch is that liquid leaves and solids do not. Whatever settles below the drain stays behind and keeps building until it has to be agitated and pumped out.
Pumping station: The point where manure is moved out of a barn pit or transferred between storages, usually a sump or receiving pit with a pump. It is where solids that will not stay in suspension show up first, plugging lines and slowing everything down. Gas concentrations run high around a station during transfer, so ventilation matters and nobody should be down in it.
Sludge: The settled solids layer in a lagoon or pit, sitting above the hardpan and thicker than the liquid over it. Sludge is partly digested and holds a large share of the phosphorus and organic nitrogen in the storage, so it is worth something when you get it out. It will pump if it is agitated well, but it hauls heavy, spreads unevenly, and throws off your application rates if you ignore it.
Volatile fatty acids (VFAs): Short-chain acids such as acetic, propionic, and butyric that form partway through anaerobic digestion. They are meant to be an intermediate step, consumed by the methane-forming bacteria about as fast as they are made. When the acid formers outrun the methane formers, VFAs build up, pH drops, and digestion slows down further. High VFA levels also show up in pits that foam, and they carry a good share of the sour smell.

How these terms fit together: how PitCharger treatment works