Biological warfare
Many viral agents have been studied and/or weaponized, including some of the Bunyaviridae (especially Rift Valley fever virus), Ebolavirus, many of the Flaviviridae (especially Japanese encephalitis virus), Machupo virus, Coronaviruses, Marburg virus, Variola virus, and yellow fever virus. Fungal agents that have been studied include Coccidioides spp.
Toxins that can be used as weapons include ricin, staphylococcal enterotoxin B, botulinum toxin, saxitoxin, and many mycotoxins. These toxins and the organisms that produce them are sometimes referred to as select agents. In the United States, their possession, use, and transfer are regulated by the Centers for Disease Control and Prevention's Select Agent Program.
The former US biological warfare program categorized its weaponized anti-personnel bio-agents as either Lethal Agents (Bacillus anthracis, Francisella tularensis, Botulinum toxin) or Incapacitating Agents (Brucella suis, Coxiella burnetii, Venezuelan equine encephalitis virus, Staphylococcal enterotoxin B).

Anti-agriculture: 

Anti-crop/anti-vegetation/anti-fisheries: The United States developed an anti-crop capability during the Cold War that used plant diseases (bioherbicides, or mycoherbicides) for destroying enemy agriculture. Biological weapons also target fisheries as well as water-based vegetation. It was believed that the destruction of enemy agriculture on a strategic scale could thwart Sino-Soviet aggression in a general war. Diseases such as wheat blast and rice blast were weaponized in aerial spray tanks and cluster bombs for delivery to enemy watersheds in agricultural regions to initiate epiphytotic (epidemics among plants). On the other hand, some sources report that these agents were stockpiled but never weaponized. When the United States renounced its offensive biological warfare program in 1969 and 1970, the vast majority of its biological arsenal was composed of these plant diseases. Enterotoxins and Mycotoxins were not affected by Nixon's order.
Though herbicides are chemicals, they are often grouped with biological warfare and chemical warfare because they may work in a similar manner as biotoxins or bioregulators.  The Army Biological Laboratory tested each agent and the Army's Technical Escort Unit was responsible for the transport of all chemical, biological, radiological (nuclear) materials.
Biological warfare can also specifically target plants to destroy crops or defoliate vegetation. The United States and Britain discovered plant growth regulators (i.e., herbicides) during the Second World War, which were then used by the UK in the counterinsurgency operations of the Malayan Emergency. Inspired by the use in Malaysia, the US military effort in the Vietnam War included a mass dispersal of a variety of herbicides, famously Agent Orange, with the aim of destroying farmland and defoliating forests used as cover by the Viet Cong. Sri Lanka deployed military defoliants in its prosecution of the Eelam War against Tamil insurgents.

Anti-livestock: During World War I, German saboteurs used anthrax and glanders to sicken cavalry horses in U.S. and France, sheep in Romania, and livestock in Argentina intended for the Entente forces. One of these German saboteurs was Anton Dilger. Also, Germany itself became a victim of similar attacks – horses bound for Germany were infected with Burkholderia by French operatives in Switzerland.
During World War II, the U.S. and Canada secretly investigated the use of rinderpest, a highly lethal disease of cattle, as a bioweapon.
In the 1980s Soviet Ministry of Agriculture had successfully developed variants of foot-and-mouth disease, and rinderpest against cows, African swine fever for pigs, and psittacosis to kill the chicken. These agents were prepared to spray them down from tanks attached to airplanes over hundreds of miles. The secret program was code-named "Ecology".
During the Mau Mau Uprising in 1952, the poisonous latex of the African milk bush was used to kill cattle.

Defensive operations: 

Medical countermeasures: In 2010 at The Meeting of the States Parties to the Convention on the Prohibition of the Development, Production and Stockpiling of Bacteriological (Biological) and Toxin Weapons and Their Destruction in Geneva
the sanitary epidemiological reconnaissance was suggested as well-tested means for enhancing the monitoring of infections and parasitic agents, for the practical implementation of the International Health Regulations (2005). The aim was to prevent and minimize the consequences of natural outbreaks of dangerous infectious diseases as well as the threat of alleged use of biological weapons against BTWC States Parties.
Many countries require their active-duty military personnel to get vaccinated for certain diseases that may potentially be used as a bioweapon such as anthrax, smallpox, and various other vaccines depending on the Area of Operations of the individual military units and commands.

Public health and disease surveillance: Most classical and modern biological weapons' pathogens can be obtained from a plant or an animal which is naturally infected.
In the largest biological weapons accident known—the anthrax outbreak in Sverdlovsk (now Yekaterinburg) in the Soviet Union in 1979—sheep became ill with anthrax as far as 200 kilometers from the release point of the organism from a military facility in the southeastern portion of the city and still off-limits to visitors today, (see Sverdlovsk Anthrax leak).
Thus, a robust surveillance system involving human clinicians and veterinarians may identify a bioweapons attack early in the course of an epidemic, permitting the prophylaxis of disease in the vast majority of people (and/or animals) exposed but not yet ill.
For example, in the case of anthrax, it is likely that by 24–36 hours after an attack, some small percentage of individuals (those with the compromised immune system or who had received a large dose of the organism due to proximity to the release point) will become ill with classical symptoms and signs (including a virtually unique chest X-ray finding, often recognized by public health officials if they receive timely reports). The incubation period for humans is estimated to be about 11.8 days to 12.1 days.  This suggested period is the first model that is independently consistent with data from the largest known human outbreak. These projections refine previous estimates of the distribution of early-onset cases after a release and support a recommended 60-day course of prophylactic antibiotic treatment for individuals exposed to low doses of anthrax. By making these data available to local public health officials in real time, most models of anthrax epidemics indicate that more than 80% of an exposed population can receive antibiotic treatment before becoming symptomatic, and thus avoid the moderately high mortality of the disease.

Common epidemiological warnings: From most specific to least specific:

Single cause of a certain disease caused by an uncommon agent, with lack of an epidemiological explanation.
Unusual, rare, genetically engineered strain of an agent.
High morbidity and mortality rates in regards to patients with the same or similar symptoms.
Unusual presentation of the disease.
Unusual geographic or seasonal distribution.
Stable endemic disease, but with an unexplained increase in relevance.
Rare transmission (aerosols, food, water).
No illness presented in people who were/are not exposed to "common ventilation systems (have separate closed ventilation systems) when illness is seen in persons in close proximity who have a common ventilation system."
Different and unexplained diseases coexisting in the same patient without any other explanation.
Rare illness that affects a large, disparate population (respiratory disease might suggest the pathogen or agent was inhaled).
Illness is unusual for a certain population or age-group in which it takes presence.
Unusual trends of death and/or illness in animal populations, previous to or accompanying illness in humans.
Many affected reaching out for treatment at the same time.
Similar genetic makeup of agents in affected individuals.
Simultaneous collections of similar illness in non-contiguous areas, domestic, or foreign.
An abundance of cases of unexplained diseases and deaths.

Bioweapon identification: The goal of biodefense is to integrate the sustained efforts of the national and homeland security, medical, public health, intelligence, diplomatic, and law enforcement communities. Health care providers and public health officers are among the first lines of defense. In some countries private, local, and provincial (state) capabilities are being augmented by and coordinated with federal assets, to provide layered defenses against biological weapon attacks. During the first Gulf War the United Nations activated a biological and chemical response team, Task Force Scorpio, to respond to any potential use of weapons of mass destruction on civilians.
The traditional approach toward protecting agriculture, food, and water: focusing on the natural or unintentional introduction of a disease is being strengthened by focused efforts to address current and anticipated future biological weapons threats that may be deliberate, multiple, and repetitive.
The growing threat of biowarfare agents and bioterrorism has led to the development of specific field tools that perform on-the-spot analysis and identification of encountered suspect materials. One such technology, being developed by researchers from the Lawrence Livermore National Laboratory (LLNL), employs a "sandwich immunoassay", in which fluorescent dye-labeled antibodies aimed at specific pathogens are attached to silver and gold nanowires.
In the Netherlands, the company TNO has designed Bioaerosol Single Particle Recognition eQuipment (BiosparQ). This system would be implemented into the national response plan for bioweapon attacks in the Netherlands.